=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderdhyV6gx/inputs/gromacs_2026.1-1_all.buildinfo Source: gromacs Version: 2026.1-1 rebuilderd-worker node: ionos25-amd64 +------------------------------------------------------------------------------+ | Downloading sources Sat, 14 Mar 2026 05:46:58 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [60.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [137 kB] Get:7 https://deb.debian.org/debian sid InRelease [187 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6552 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [148 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [194 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [163 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2464 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [8304 B] Get:18 https://deb.debian.org/debian forky/main Sources [10.7 MB] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.5 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.5 MB] Get:21 https://deb.debian.org/debian experimental/non-free-firmware Sources [2568 B] Get:22 https://deb.debian.org/debian experimental/main Sources [445 kB] Fetched 34.5 MB in 32s (1075 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.1-1.dsc' gromacs_2026.1-1.dsc 3267 SHA256:18bc640c5e9bc2c65b1475036efa60987d4f4171281824c2caed1b5f8a752569 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.1.orig-regressiontests.tar.gz' gromacs_2026.1.orig-regressiontests.tar.gz 16580717 SHA256:dbdcc50bf1c1b590adeacfd5cf187f805bf4238aaf63cd05bb8958b49c1afd44 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.1.orig.tar.gz' gromacs_2026.1.orig.tar.gz 45914061 SHA256:d95a313f56db7e05ee3a21e50f582fdee5176c2f60b900bab2461fd95c5e81be 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.1-1.debian.tar.xz' gromacs_2026.1-1.debian.tar.xz 37208 SHA256:129934c052865fc9ebb7f684a865f792f49f9f24ae6a82ca64efac25ee846272 dbdcc50bf1c1b590adeacfd5cf187f805bf4238aaf63cd05bb8958b49c1afd44 gromacs_2026.1.orig-regressiontests.tar.gz d95a313f56db7e05ee3a21e50f582fdee5176c2f60b900bab2461fd95c5e81be gromacs_2026.1.orig.tar.gz 129934c052865fc9ebb7f684a865f792f49f9f24ae6a82ca64efac25ee846272 gromacs_2026.1-1.debian.tar.xz 18bc640c5e9bc2c65b1475036efa60987d4f4171281824c2caed1b5f8a752569 gromacs_2026.1-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Sat, 14 Mar 2026 05:47:31 +0000 | +------------------------------------------------------------------------------+ + niceRebuilding gromacs=2026.1-1 in /srv/rebuilderd/tmp/rebuilderdhyV6gx/inputs now. /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdhyV6gx/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdhyV6gx/inputs/gromacs_2026.1-1_all.buildinfo /srv/rebuilderd/tmp/rebuilderdhyV6gx/inputs/gromacs_2026.1-1_all.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/gromacs-2026.1 I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable InRelease [187 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages [10.3 MB] Get:4 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 Packages [10.3 MB] Fetched 21.1 MB in 2s (8706 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260310T023034Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 16-20260308-1 [151 kB] Fetched 151 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiu5c_b9j/libgomp1_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblz4-1 amd64 1.10.0-8 [70.1 kB] Fetched 70.1 kB in 0s (6725 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqfrbg7si/liblz4-1_1.10.0-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.9.1-1 [17.4 kB] Fetched 17.4 kB in 0s (1723 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph9du1byt/libcap-ng0_0.9.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libperl5.40 amd64 5.40.1-7 [4317 kB] Fetched 4317 kB in 0s (134 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgnmhwlx0/libperl5.40_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 adduser all 3.154 [210 kB] Fetched 210 kB in 0s (18.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx19fl9kr/adduser_3.154_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b3 [16.7 kB] Fetched 16.7 kB in 0s (1407 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4gtq8m_2/libpaper2_2.2.5-0.3+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-4 [74.8 kB] Fetched 74.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp47oj7u_x/readline-common_8.3-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.7 [1531 kB] Fetched 1531 kB in 0s (85.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx8a4_wr0/dpkg_1.23.7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.16-1+b1 [195 kB] Fetched 195 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpop_en3x5/libde265-0_1.0.16-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-copybutton all 0.5.2-3 [18.1 kB] Fetched 18.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx4l_6klj/python3-sphinx-copybutton_0.5.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.131-1 [39.9 kB] Fetched 39.9 kB in 0s (3761 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc4k9sxv0/libdrm2_2.4.131-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0jfvtcm/python3-chardet_5.2.0+dfsg-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5+b1 [199 kB] Fetched 199 kB in 0s (17.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxs57xr4n/liblerc4_4.0.0+ds-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [138 kB] Fetched 138 kB in 0s (13.4 MB/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpun1oehjv/python3-numpy-dev_2.3.5+ds-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1+b1 [36.7 kB] Fetched 36.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjv6f3gzi/libnuma-dev_2.0.19-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Fetched 10.5 kB in 0s (866 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2vjjyast/libpython3-stdlib_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 16-20260308-1 [765 kB] Fetched 765 kB in 0s (54.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpriii1qi6/libstdc++6_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-accessible-pygments all 0.0.5-2 [1306 kB] Fetched 1306 kB in 0s (82.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzmnb3srl/python3-accessible-pygments_0.0.5-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.06.0~dfsg-3 [50.6 kB] Fetched 50.6 kB in 0s (4785 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7km4gt7d/ghostscript_10.06.0~dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9+b1 [883 kB] Fetched 883 kB in 0s (53.8 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp58g3k1e1/procps_4.0.4-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-2+b1 [132 kB] Fetched 132 kB in 0s (11.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpejo_s0ge/libbsd0_0.12.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwy1t64 amd64 1.3.0-2 [709 kB] Fetched 709 kB in 0s (53.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzzxwbp8p/libhwy1t64_1.3.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4+b1 [36.7 kB] Fetched 36.7 kB in 0s (2696 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwbmokvpx/libmpfi0_1.5.4+ds-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.2.3-12 [478 kB] Fetched 478 kB in 0s (38.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn9qfiw5p/python3-sphinx_8.2.3-12_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 graphviz amd64 14.1.2-1 [60.6 kB] Fetched 60.6 kB in 0s (5866 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpymxbovto/graphviz_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Fetched 641 kB in 0s (49.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdennogo4/libxml2-16_2.15.1+dfsg-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Fetched 829 kB in 0s (60.8 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp730of0bb/libx11-6_1.8.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp631ijmv0/pkgconf_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 9.0.2-4 [273 kB] Fetched 273 kB in 0s (24.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpncrbj1dl/python3-pytest_9.0.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [7487 kB] Fetched 7487 kB in 0s (154 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.3.5+ds-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpiv_fey43/python3-numpy_2.3.5+ds-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgvplugin-gd8 amd64 14.1.2-1 [27.3 kB] Fetched 27.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp46hqial2/libgvplugin-gd8_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1.1 [135 kB] Fetched 135 kB in 0s (13.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprj_f_svb/librhash1_1.4.6-1.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.41.3-4 [39.1 kB] Fetched 39.1 kB in 0s (3789 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7zhyeveg/libuuid1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mawk amd64 1.3.4.20260302-1 [142 kB] Fetched 142 kB in 0s (13.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2n5u0lzz/mawk_1.3.4.20260302-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b2 [108 kB] Fetched 108 kB in 0s (10.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_a5nx_s/libevent-extra-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-5+b1 [11.3 MB] Fetched 11.3 MB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg9eh2hno/libboost1.90-dev_1.90.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcdt6 amd64 14.1.2-1 [18.6 kB] Fetched 18.6 kB in 0s (70.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg3wdusij/libcdt6_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.2.0-15 [18.6 kB] Fetched 18.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz7pnuk9x/gfortran-15_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 16-20260308-1 [1580 kB] Fetched 1580 kB in 0s (91.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf0n7mfjn/libhwasan0_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebconfclient0 amd64 0.282+b2 [11.2 kB] Fetched 11.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7p2czpki/libdebconfclient0_0.282+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc amd64 4:15.2.0-5 [5160 B] Fetched 5160 B in 0s (0 B/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp9ogvz4gx/gcc_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp amd64 4:15.2.0-5 [1564 B] Fetched 1564 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpy42ksv7c/cpp_15.2.0-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 dh-python all 7.20260125 [119 kB] Fetched 119 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbafup6_2/dh-python_7.20260125_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (26.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqi6p2iuy/sed_4.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.4-1 [206 kB] Fetched 206 kB in 0s (14.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoqzb0lb5/libopenjp2-7_2.5.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 furo all 2025.12.19+dfsg-1 [62.2 kB] Fetched 62.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd9st0e46/furo_2025.12.19+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.21.0-1 [136 kB] Fetched 136 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiljqmsy9/libngtcp2-16_1.21.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Fetched 480 kB in 0s (43.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8v1ka41h/libunistring5_1.4.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b2 [2095 kB] Fetched 2095 kB in 0s (112 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplosmevza/libfftw3-dev_3.3.10-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 graphicsmagick amd64 1.4+really1.3.46-2 [1102 kB] Fetched 1102 kB in 0s (69.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwetgy4dc/graphicsmagick_1.4+really1.3.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.4-2 [171 kB] Fetched 171 kB in 0s (16.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp26o4kmhx/python3-charset-normalizer_3.4.4-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-5 [28.3 MB] Fetched 28.3 MB in 1s (37.0 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp4qkrn_dq/libllvm21_21.1.8-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.46-3 [548 kB] Fetched 548 kB in 0s (1799 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5v76gr_8/libbinutils_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpgk8mk_mr/libxdmcp6_1.1.5-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.20 [3504 B] Fetched 3504 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6y6r1os3/mpi-default-dev_1.20_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.46-3 [92.2 kB] Fetched 92.2 kB in 0s (8275 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzmrl0xze/libctf0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (22.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphgrkxx0q/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.10-1 [1028 kB] Fetched 1028 kB in 0s (65.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rtq5eea/libopenmpi-dev_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-18 [45.2 kB] Fetched 45.2 kB in 0s (3384 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2ike129/libavahi-common3_0.8-18_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tar amd64 1.35+dfsg-4 [817 kB] Fetched 817 kB in 0s (60.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprahqaxhf/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-13 [1123 kB] Fetched 1123 kB in 0s (75.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy6r5pmju/libc-gconv-modules-extra_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.16.0-2+b1 [79.3 kB] Fetched 79.3 kB in 0s (7515 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0np6pgg9/libfido2-1_1.16.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.43-2+b1 [49.0 kB] Fetched 49.0 kB in 0s (4721 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt8ngxb06/libidn12_1.43-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mscgen amd64 0.20-16 [46.8 kB] Fetched 46.8 kB in 0s (4147 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsvwi9sh3/mscgen_0.20-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.22.4+dfsg-1 [128 kB] Fetched 128 kB in 0s (11.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxx0j47k2/docutils-common_0.22.4+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Fetched 1469 kB in 0s (87.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkvco2pdf/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.21.2-3 [650 kB] Fetched 650 kB in 0s (49.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbqkl23_9/libheif1_1.21.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-2 [6052 kB] Fetched 6052 kB in 0s (147 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwi_jzjvc/python-babel-localedata_2.17.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.17.1-5 [132 kB] Fetched 132 kB in 0s (12.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpru3empc2/libfontconfig1_2.17.1-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp457nn_m1/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-3 [544 kB] Fetched 544 kB in 0s (40.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvvrwc2ca/libcairo2_1.18.4-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsframe3 amd64 2.46-3 [84.7 kB] Fetched 84.7 kB in 0s (8259 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp66qum38/libsframe3_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-5 [1436 B] Fetched 1436 B in 0s (138 kB/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpzwbjvka7/gcc-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ax3bjvs/libacl1_2.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgav1-2 amd64 0.20.0-2 [373 kB] Fetched 373 kB in 0s (32.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp7mas79i/libgav1-2_0.20.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [36.1 kB] Fetched 36.1 kB in 0s (3488 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_abr7dsm/libpangocairo-1.0-0_1.57.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4+b1 [128 kB] Fetched 128 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq2ybjv5x/libfmt10_10.1.1+ds1-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.13.0-2 [165 kB] Fetched 165 kB in 0s (16.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ynbht13/libhwloc15_2.13.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Fetched 181 kB in 0s (17.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppkweas4n/libpsm2-2_11.2.185-2.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 openssl-provider-legacy amd64 3.5.5-1 [311 kB] Fetched 311 kB in 0s (30.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ylg9gj3/openssl-provider-legacy_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (2216 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpbg9m_3r5/libattr1_2.5.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-5 [82.6 kB] Fetched 82.6 kB in 0s (415 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpva__cs76/libjsoncpp26_1.9.6-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Fetched 168 kB in 0s (459 kB/s) dpkg-name: info: moved 'libjpeg62-turbo_1%3a2.1.5-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpe9_3ktl4/libjpeg62-turbo_2.1.5-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5+b2 [156 kB] Fetched 156 kB in 0s (722 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwlphu8gd/libkpathsea6_2025.20250727.75242+ds-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2+b1 [28.1 kB] Fetched 28.1 kB in 0s (468 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdfj7u43x/libxxhash0_0.8.3-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2025.20260124-1 [8520 kB] Fetched 8520 kB in 0s (157 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6mggqbx7/texlive-latex-recommended_2025.20260124-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 libze1 amd64 1.28.2-1 [793 kB] Fetched 793 kB in 0s (54.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6kd544ly/libze1_1.28.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026a-1 [259 kB] Fetched 259 kB in 0s (25.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplzrhwucv/tzdata_2026a-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.8.3-1 [39.6 kB] Fetched 39.6 kB in 0s (3586 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppn2y1ly2/python3-soupsieve_2.8.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Fetched 678 kB in 0s (50.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa6cm05zx/libhsa-runtime64-1_6.4.3+dfsg-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5+b1 [70.4 kB] Fetched 70.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3xjud46v/libpam0g_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.68.0-2 [79.2 kB] Fetched 79.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp290b4lmc/libnghttp2-14_1.68.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.90.0.1 [3048 B] Fetched 3048 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi2in_pdz/libboost-dev_1.90.0.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 16-20260308-1 [2573 kB] Fetched 2573 kB in 0s (102 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_f20_cr/libtsan2_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-3 [89.0 kB] Fetched 89.0 kB in 0s (6535 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpoeknoyzz/zlib1g_1.3.dfsg+really1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Fetched 13.9 MB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd8o5mq8r/libamd-comgr3_7.0.2+dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Fetched 307 kB in 0s (27.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfe53mcyv/libnettle8t64_3.10.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Fetched 1601 kB in 0s (84.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_2xt_eyu/poppler-data_0.4.12-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-13+b1 [127 kB] Fetched 127 kB in 0s (12.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj4vgics7/libgd3_2.3.3-13+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1+b1 [245 kB] Fetched 245 kB in 0s (24.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfxsl2pk2/libssh2-1t64_1.11.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-15 [13.1 MB] Fetched 13.1 MB in 0s (160 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg4lsg9_d/g++-15-x86-64-linux-gnu_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7zpo8_8b/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.30-1 [172 kB] Fetched 172 kB in 0s (16.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp638yf8fy/libthai-data_0.1.30-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 kB] Fetched 26.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0cjgyoof/libffi8_3.5.2-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Fetched 62.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpks9n5es3/t1utils_1.41-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm-compat4t64 amd64 1.26-1+b1 [53.1 kB] Fetched 53.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo38kqvf3/libgdbm-compat4t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Fetched 57.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbxmg__sh/libsasl2-2_2.1.28+dfsg1-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b1 [66.1 kB] Fetched 66.1 kB in 0s (6586 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-9+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmppw00ajz5/libproc2-0_4.0.4-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsepol2 amd64 3.9-2 [300 kB] Fetched 300 kB in 0s (22.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjyiq1v2i/libsepol2_3.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 libsystemd0 amd64 260~rc2-1 [446 kB] Fetched 446 kB in 0s (35.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptx5mo_n0/libsystemd0_260~rc2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2025.20250727.75242+ds-5+b2 [51.4 kB] Fetched 51.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphcr36oxl/libptexenc1_2025.20250727.75242+ds-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.2.3-2 [2556 kB] Fetched 2556 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfmzdfjpz/cmake-data_4.2.3-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 61.0-2 [686 kB] Fetched 686 kB in 0s (52.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5jt2juxp/libibverbs-dev_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.6.3-1 [120 kB] Fetched 120 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq6jms18q/python3-urllib3_2.6.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgraphicsmagick-q16-3t64 amd64 1.4+really1.3.46-2 [1267 kB] Fetched 1267 kB in 0s (75.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbfq2mev9/libgraphicsmagick-q16-3t64_1.4+really1.3.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkvp0lgps/coreutils_9.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Fetched 33.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp63iys83l/libkrb5support0_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.9-4+b1 [86.1 kB] Fetched 86.1 kB in 0s (6207 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp34aj7kyj/libselinux1_3.9-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.46-3 [820 kB] Fetched 820 kB in 0s (64.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqc028m26/libgprofng0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-15 [2719 kB] Fetched 2719 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8_6wvep/libgcc-15-dev_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.12-1 [5298 kB] Fetched 5298 kB in 0s (145 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyujdwpud/libpython3.13-dev_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b2 [105 kB] Fetched 105 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzfqt4ez7/libxcb-shm0_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.7.0~rc1-1 [329 kB] Fetched 329 kB in 0s (30.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph_c0nfwh/libucc1_1.7.0~rc1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3870l9ri/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.12-1 [504 kB] Fetched 504 kB in 0s (46.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb4so9pyb/python3.13-dev_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libspdlog1.15 amd64 1:1.15.3+ds-1+b1 [109 kB] Fetched 109 kB in 0s (0 B/s) dpkg-name: info: moved 'libspdlog1.15_1%3a1.15.3+ds-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpw95ai_g8/libspdlog1.15_1.15.3+ds-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1+b1 [37.9 kB] Fetched 37.9 kB in 0s (386 kB/s) dpkg-name: info: moved 'libsm6_2%3a1.2.6-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp01op0c64/libsm6_1.2.6-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Fetched 5852 B in 0s (539 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpowofcqkq/libapache-pom-java_33-2_all.deb' Downloading dependency 1 of 466: libgomp1:amd64=16-20260308-1 Downloading dependency 2 of 466: liblz4-1:amd64=1.10.0-8 Downloading dependency 3 of 466: libcap-ng0:amd64=0.9.1-1 Downloading dependency 4 of 466: libperl5.40:amd64=5.40.1-7 Downloading dependency 5 of 466: adduser:amd64=3.154 Downloading dependency 6 of 466: libpaper2:amd64=2.2.5-0.3+b3 Downloading dependency 7 of 466: readline-common:amd64=8.3-4 Downloading dependency 8 of 466: dpkg:amd64=1.23.7 Downloading dependency 9 of 466: libde265-0:amd64=1.0.16-1+b1 Downloading dependency 10 of 466: python3-sphinx-copybutton:amd64=0.5.2-3 Downloading dependency 11 of 466: libdrm2:amd64=2.4.131-1 Downloading dependency 12 of 466: python3-chardet:amd64=5.2.0+dfsg-2 Downloading dependency 13 of 466: liblerc4:amd64=4.0.0+ds-5+b1 Downloading dependency 14 of 466: python3-numpy-dev:amd64=1:2.3.5+ds-3 Downloading dependency 15 of 466: libnuma-dev:amd64=2.0.19-1+b1 Downloading dependency 16 of 466: libpython3-stdlib:amd64=3.13.9-3 Downloading dependency 17 of 466: libstdc++6:amd64=16-20260308-1 Downloading dependency 18 of 466: python3-accessible-pygments:amd64=0.0.5-2 Downloading dependency 19 of 466: ghostscript:amd64=10.06.0~dfsg-3 Downloading dependency 20 of 466: procps:amd64=2:4.0.4-9+b1 Downloading dependency 21 of 466: libbsd0:amd64=0.12.2-2+b1 Downloading dependency 22 of 466: libhwy1t64:amd64=1.3.0-2 Downloading dependency 23 of 466: libmpfi0:amd64=1.5.4+ds-4+b1 Downloading dependency 24 of 466: python3-sphinx:amd64=8.2.3-12 Downloading dependency 25 of 466: graphviz:amd64=14.1.2-1 Downloading dependency 26 of 466: libxml2-16:amd64=2.15.1+dfsg-2+b1 Downloading dependency 27 of 466: libx11-6:amd64=2:1.8.13-1 Downloading dependency 28 of 466: pkgconf:amd64=2.5.1-4 Downloading dependency 29 of 466: python3-pytest:amd64=9.0.2-4 Downloading dependency 30 of 466: python3-numpy:amd64=1:2.3.5+ds-3 Downloading dependency 31 of 466: libgvplugin-gd8:amd64=14.1.2-1 Downloading dependency 32 of 466: librhash1:amd64=1.4.6-1.1 Downloading dependency 33 of 466: libuuid1:amd64=2.41.3-4 Downloading dependency 34 of 466: mawk:amd64=1.3.4.20260302-1 Downloading dependency 35 of 466: libevent-extra-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 36 of 466: libboost1.90-dev:amd64=1.90.0-5+b1 Downloading dependency 37 of 466: libcdt6:amd64=14.1.2-1 Downloading dependency 38 of 466: gfortran-15:amd64=15.2.0-15 Downloading dependency 39 of 466: libhwasan0:amd64=16-20260308-1 Downloading dependency 40 of 466: libdebconfclient0:amd64=0.282+b2 Downloading dependency 41 of 466: gcc:amd64=4:15.2.0-5 Downloading dependency 42 of 466: cpp:amd64=4:15.2.0-5 Downloading dependency 43 of 466: dh-python:amd64=7.20260125 Downloading dependency 44 of 466: sed:amd64=4.9-2 Downloading dependency 45 of 466: libopenjp2-7:amd64=2.5.4-1 Downloading dependency 46 of 466: furo:amd64=2025.12.19+dfsg-1 Downloading dependency 47 of 466: libngtcp2-16:amd64=1.21.0-1 Downloading dependency 48 of 466: libunistring5:amd64=1.4.2-1 Downloading dependency 49 of 466: libfftw3-dev:amd64=3.3.10-2+b2 Downloading dependency 50 of 466: graphicsmagick:amd64=1.4+really1.3.46-2 Downloading dependency 51 of 466: python3-charset-normalizer:amd64=3.4.4-2 Downloading dependency 52 of 466: libllvm21:amd64=1:21.1.8-5 Downloading dependency 53 of 466: libbinutils:amd64=2.46-3 Downloading dependency 54 of 466: libxdmcp6:amd64=1:1.1.5-2 Downloading dependency 55 of 466: mpi-default-dev:amd64=1.20 Downloading dependency 56 of 466: libctf0:amd64=2.46-3 Downloading dependency 57 of 466: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 58 of 466: libopenmpi-dev:amd64=5.0.10-1 Downloading dependency 59 of 466: libavahi-common3:amd64=0.8-18 Downloading dependency 60 of 466: tar:amd64=1.35+dfsg-4 Downloading dependency 61 of 466: libc-gconv-modules-extra:amd64=2.42-13 Downloading dependency 62 of 466: libfido2-1:amd64=1.16.0-2+b1 Downloading dependency 63 of 466: libidn12:amd64=1.43-2+b1 Downloading dependency 64 of 466: mscgen:amd64=0.20-16 Downloading dependency 65 of 466: docutils-common:amd64=0.22.4+dfsg-1 Downloading dependency 66 of 466: man-db:amd64=2.13.1-1 Downloading dependency 67 of 466: libheif1:amd64=1.21.2-3 Downloading dependency 68 of 466: python-babel-localedata:amd64=2.17.0-2 Downloading dependency 69 of 466: libfontconfig1:amd64=2.17.1-5 Downloading dependency 70 of 466: debconf:amd64=1.5.92 Downloading dependency 71 of 466: libcairo2:amd64=1.18.4-3 Downloading dependency 72 of 466: libsframe3:amd64=2.46-3 Downloading dependency 73 of 466: gcc-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 74 of 466: libacl1:amd64=2.3.2-3 Downloading dependency 75 of 466: libgav1-2:amd64=0.20.0-2 Downloading dependency 76 of 466: libpangocairo-1.0-0:amd64=1.57.0-1 Downloading dependency 77 of 466: libfmt10:amd64=10.1.1+ds1-4+b1 Downloading dependency 78 of 466: libhwloc15:amd64=2.13.0-2 Downloading dependency 79 of 466: libpsm2-2:amd64=11.2.185-2.1 Downloading dependency 80 of 466: openssl-provider-legacy:amd64=3.5.5-1 Downloading dependency 81 of 466: libattr1:amd64=1:2.5.2-4 Downloading dependency 82 of 466: libjsoncpp26:amd64=1.9.6-5 Downloading dependency 83 of 466: libjpeg62-turbo:amd64=1:2.1.5-4 Downloading dependency 84 of 466: libkpathsea6:amd64=2025.20250727.75242+ds-5+b2 Downloading dependency 85 of 466: libxxhash0:amd64=0.8.3-2+b1 Downloading dependency 86 of 466: texlive-latex-recommended:amd64=2025.20260124-1 Downloading dependency 87 of 466: libze1:amd64=1.28.2-1 Downloading dependency 88 of 466: tzdata:amd64=2026a-1 Downloading dependency 89 of 466: python3-soupsieve:amd64=2.8.3-1 Downloading dependency 90 of 466: libhsa-runtime64-1:amd64=6.4.3+dfsg-5 Downloading dependency 91 of 466: libpam0g:amd64=1.7.0-5+b1 Downloading dependency 92 of 466: libnghttp2-14:amd64=1.68.0-2 Downloading dependency 93 of 466: libboost-dev:amd64=1.90.0.1 Downloading dependency 94 of 466: libtsan2:amd64=16-20260308-1 Downloading dependency 95 of 466: zlib1g:amd64=1:1.3.dfsg+really1.3.1-3 Downloading dependency 96 of 466: libamd-comgr3:amd64=7.0.2+dfsg-3 Downloading dependency 97 of 466: libnettle8t64:amd64=3.10.2-1 Downloading dependency 98 of 466: poppler-data:amd64=0.4.12-1 Downloading dependency 99 of 466: libgd3:amd64=2.3.3-13+b1 Downloading dependency 100 of 466: libssh2-1t64:amd64=1.11.1-1+b1 Downloading dependency 101 of 466: g++-15-x86-64-linux-gnu:amd64=15.2.0-15 Downloading dependency 102 of 466: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 103 of 466: libthai-data:amd64=0.1.30-1 Downloading dependency 104 of 466: libffi8:amd64=3.5.2-3+b1 Downloading dependency 105 of 466: t1utils:amd64=1.41-4 Downloading dependency 106 of 466: libgdbm-compat4t64:amd64=1.26-1+b1 Downloading dependency 107 of 466: libsasl2-2:amd64=2.1.28+dfsg1-10 Downloading dependency 108 of 466: libproc2-0:amd64=2:4.0.4-9+b1 Downloading dependency 109 of 466: libsepol2:amd64=3.9-2 Downloading dependency 110 of 466: libsystemd0:amd64=260~rc2-1 Downloading dependency 111 of 466: libptexenc1:amd64=2025.20250727.75242+ds-5+b2 Downloading dependency 112 of 466: cmake-data:amd64=4.2.3-2 Downloading dependency 113 of 466: libibverbs-dev:amd64=61.0-2 Downloading dependency 114 of 466: python3-urllib3:amd64=2.6.3-1 Downloading dependency 115 of 466: libgraphicsmagick-q16-3t64:amd64=1.4+really1.3.46-2 Downloading dependency 116 of 466: coreutils:amd64=9.10-1 Downloading dependency 117 of 466: libkrb5support0:amd64=1.22.1-2 Downloading dependency 118 of 466: libselinux1:amd64=3.9-4+b1 Downloading dependency 119 of 466: libgprofng0:amd64=2.46-3 Downloading dependency 120 of 466: libgcc-15-dev:amd64=15.2.0-15 Downloading dependency 121 of 466: libpython3.13-dev:amd64=3.13.12-1 Downloading dependency 122 of 466: libxcb-shm0:amd64=1.17.0-2+b2 Downloading dependency 123 of 466: libucc1:amd64=1.7.0~rc1-1 Downloading dependency 124 of 466: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 125 of 466: python3.13-dev:amd64=3.13.12-1 Downloading dependency 126 of 466: libspdlog1.15:amd64=1:1.15.3+ds-1+b1 Downloading dependency 127 of 466: libsm6:amd64=2:1.2.6-1+b1 Downloading dependency 128 of 466: libapache-pom-java:amd64=33-2 Downloading dependency 129 of 466: liblapack3:amd64=3.12.1-7+b1Get:1 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7+b1 [2550 kB] Fetched 2550 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc0286k_3/liblapack3_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-inline-tabs all 2023.4.21-3 [36.0 kB] Fetched 36.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt_bg2qat/python3-sphinx-inline-tabs_2023.4.21-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Fetched 332 kB in 0s (30.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprx15tc76/m4_1.4.21-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.14.2+dfsg-1 [492 kB] Fetched 492 kB in 0s (41.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxa9pfj0u/libfreetype6_2.14.2+dfsg-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Fetched 540 kB in 0s (45.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2olrjp77/libtool_2.5.4-9_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5 [5324 B] Fetched 5324 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpyy805o3d/cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b3 [32.2 kB] Fetched 32.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn2d87ass/libjbig0_2.1-6.1+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2025.20260124-1 [4992 kB] Fetched 4992 kB in 0s (144 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwd83z8_8/texlive-fonts-recommended_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2026.2.25+ds-1 [9612 B] Fetched 9612 B in 0s (928 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb1p3xclu/python3-certifi_2026.2.25+ds-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.06.0~dfsg-3 [479 kB] Fetched 479 kB in 0s (44.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiv04aejl/libgs10-common_10.06.0~dfsg-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (25.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv2i12iyw/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpavzzb6v5/xml-core_0.19_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsemanage2 amd64 3.9-1+b1 [96.9 kB] Fetched 96.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl9num9y2/libsemanage2_3.9-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 61.0-2 [73.0 kB] Fetched 73.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwobx3qf5/librdmacm1t64_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15 amd64 15.2.0-15 [537 kB] Fetched 537 kB in 0s (44.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7oaqjv73/gcc-15_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (49.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4py7yvay/findutils_4.10.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-16-base amd64 16-20260308-1 [35.3 kB] Fetched 35.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7fnv1dpb/gcc-16-base_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmppy58taa9/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1+b1 [126 kB] Fetched 126 kB in 0s (12.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp10ypmx6/libwebpmux3_1.5.0-0.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 patch amd64 2.8-2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwdzm_cfj/patch_2.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-9 [416 kB] Fetched 416 kB in 0s (36.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpter2_xyu/libltdl7_2.5.4-9_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+26 [217 kB] Fetched 217 kB in 0s (19.8 MB/s) dpkg-name: info: moved 'x11-common_1%3a7.7+26_all.deb' to '/srv/rebuilderd/tmp/tmpma_m08_x/x11-common_7.7+26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1+b1 [66.8 kB] Fetched 66.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libice6_2%3a1.1.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp2mawh55f/libice6_1.1.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Fetched 10.8 kB in 0s (907 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl4mn7ds3/libcommons-parent-java_56-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b2 [308 kB] Fetched 308 kB in 0s (30.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpruso6gr5/libevent-dev_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-files amd64 14 [72.9 kB] Fetched 72.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph1vr3fjj/base-files_14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 16-20260308-1 [45.5 kB] Fetched 45.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf0jakjfz/libcc1-0_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Fetched 12.2 kB in 0s (947 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvwhide56/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.41.3-4 [164 kB] Fetched 164 kB in 0s (15.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfp7jarq6/mount_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-18 [49.2 kB] Fetched 49.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp16a75i74/libavahi-client3_0.8-18_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Fetched 338 kB in 0s (20.6 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp_rwq4irr/libmagic-mgc_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-3 [919 kB] Fetched 919 kB in 0s (64.3 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpa78_fcft/zlib1g-dev_1.3.dfsg+really1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Fetched 110 kB in 0s (10.6 MB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpsljhktv0/libmagic1t64_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Fetched 4540 kB in 0s (137 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3e38npca/fonts-lmodern_2.005-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sysvinit-utils amd64 3.15-6 [35.0 kB] Fetched 35.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmlrjpydt/sysvinit-utils_3.15-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5+b1 [179 kB] Fetched 179 kB in 0s (17.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxzizhwhg/libpam-modules_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpriki_ajo/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxapian30 amd64 1.4.31-2 [1172 kB] Fetched 1172 kB in 0s (73.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8nb4rnsp/libxapian30_1.4.31-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1+b1 [215 kB] Fetched 215 kB in 0s (19.4 MB/s) dpkg-name: info: moved 'libxaw7_2%3a1.0.16-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmptcg5odrf/libxaw7_1.0.16-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Fetched 2489 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps1oy0p7q/libsvtav1enc2_2.3.0+dfsg-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Fetched 107 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_ml59ki/python3-jinja2_3.1.6-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.2.0-15 [885 kB] Fetched 885 kB in 0s (45.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyvr23df4/libgfortran-15-dev_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Fetched 98.0 kB in 0s (8326 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpmt70cpwi/libcrypt1_4.5.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b1 [716 kB] Fetched 716 kB in 0s (52.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvy65psc7/libfabric1_2.1.0-1.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b4 [52.1 kB] Fetched 52.1 kB in 0s (5047 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjo94k85g/libpciaccess0_0.17-3+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15 amd64 15.2.0-15 [1276 B] Fetched 1276 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp03jgjwwm/cpp-15_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1922.20260106-1 [176 kB] Fetched 176 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp8bm7tb0/libyuv0_0.0.1922.20260106-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1.1 [350 kB] Fetched 350 kB in 0s (31.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiwvj29rs/preview-latex-style_13.2-1.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.46.4-1+b1 [259 kB] Fetched 259 kB in 0s (23.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ltept0n/libpixman-1-0_0.46.4-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.19.2+dfsg-1 [847 kB] Fetched 847 kB in 0s (58.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkp35m8xi/python3-pygments_2.19.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (458 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwvoixj3s/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Fetched 710 kB in 0s (52.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6bjhgd8b/libdb5.3t64_5.3.28+dfsg2-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (8146 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp52cszfsv/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2 [200 kB] Fetched 200 kB in 0s (14.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8bmnet9k/libnl-route-3-200_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 3.0.1-3 [251 kB] Fetched 251 kB in 0s (23.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjpf9p6ws/python3-pybind11_3.0.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 16-20260308-1 [1280 kB] Fetched 1280 kB in 0s (71.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxunxn12f/liblsan0_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [59.2 kB] Fetched 59.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplqqjnqg2/libzzip-0-13t64_0.13.78+dfsg.1-0.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.16-1 [254 kB] Fetched 254 kB in 0s (21.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprt203ka7/libcups2t64_2.4.16-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.1-1+b1 [258 kB] Fetched 258 kB in 0s (24.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbgi0t_08/libimagequant0_4.4.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 libcurl4t64 amd64 8.19.0~rc3-1 [408 kB] Fetched 408 kB in 0s (35.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptfiemkfi/libcurl4t64_8.19.0~rc3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tex-gyre all 20180621-7 [6209 kB] Fetched 6209 kB in 0s (144 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo2vnw4gn/tex-gyre_20180621-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 16-20260308-1 [10.5 kB] Fetched 10.5 kB in 0s (1017 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph54bzic3/libatomic1_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Fetched 139 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxmi0qeyr/libgssapi-krb5-2_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7+b1 [5228 kB] Fetched 5228 kB in 0s (135 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph2vt3uq1/liblapack-dev_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Fetched 93.3 kB in 0s (7187 kB/s) dpkg-name: info: moved 'xfonts-utils_1%3a7.7+7_amd64.deb' to '/srv/rebuilderd/tmp/tmpjxxexboa/xfonts-utils_7.7+7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Fetched 337 kB in 0s (27.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphehl2kuk/libkrb5-3_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-15 [12.1 MB] Fetched 12.1 MB in 0s (170 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzto7wdef/cpp-15-x86-64-linux-gnu_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Fetched 8812 B in 0s (877 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmd44mqye/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b2 [59.8 kB] Fetched 59.8 kB in 0s (5886 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptbucl_14/libpsl5t64_0.21.2-1.1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-2 [79.8 kB] Fetched 79.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libxi6_2%3a1.8.2-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpjxh4c7ql/libxi6_1.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-2 [3654 kB] Fetched 3654 kB in 0s (131 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplopjf_kg/libprrte-dev_3.0.13-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Fetched 320 kB in 0s (26.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuim0o6l3/libbrotli1_1.2.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcgraph8 amd64 14.1.2-1 [58.8 kB] Fetched 58.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwda1pg8v/libcgraph8_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.1-1 [361 kB] Fetched 361 kB in 0s (31.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprnkcj7yf/libtiff6_4.7.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Fetched 72.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk4j9yb9w/python3-requests_2.32.5+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Fetched 154 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg6lk1v18/openmpi-bin_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b1 [22.5 kB] Fetched 22.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmah8hmie/libnuma1_2.0.19-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2025.20260124-1 [23.1 MB] Fetched 23.1 MB in 0s (83.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_69lk65t/texlive-base_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.8.5-1 [362 kB] Fetched 362 kB in 0s (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcq008jyl/libarchive13t64_3.8.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2025.20250727.75242+ds-5+b2 [8670 kB] Fetched 8670 kB in 0s (142 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp87725z1f/texlive-binaries_2025.20250727.75242+ds-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2+b1 [156 kB] Fetched 156 kB in 0s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvh6lv9h1/libuv1t64_1.51.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 3.0.3-1+b1 [14.3 kB] Fetched 14.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj_3_2w6q/python3-markupsafe_3.0.3-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Fetched 9385 kB in 0s (159 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm76h71e5/libamdhip64-6_6.4.3-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl amd64 5.40.1-7 [267 kB] Fetched 267 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4rhxwg_s/perl_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-15 [35.9 kB] Fetched 35.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwp72ynwk/gcc-15-base_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3+b1 [191 kB] Fetched 191 kB in 0s (18.6 MB/s) dpkg-name: info: moved 'libxt6t64_1%3a1.2.1-1.3+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmptww7b_ye/libxt6t64_1.2.1-1.3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Fetched 5527 kB in 0s (143 MB/s) dpkg-name: info: moved 'libpdfbox-java_1%3a1.8.16-5_all.deb' to '/srv/rebuilderd/tmp/tmpetf3k732/libpdfbox-java_1.8.16-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xz-utils amd64 5.8.2-2 [706 kB] Fetched 706 kB in 0s (56.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5sscqrk9/xz-utils_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1 [43.0 kB] Fetched 43.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnentat_4/ocl-icd-libopencl1_2.3.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5+b2 [113 kB] Fetched 113 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7du5u6ti/libtexlua53-5_2025.20250727.75242+ds-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdnq7fyy5/libevent-core-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.3-1+b1 [564 kB] Fetched 564 kB in 0s (48.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp6pwsmd7/libdav1d7_1.5.3-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bzip2 amd64 1.0.8-6+b1 [41.0 kB] Fetched 41.0 kB in 0s (4090 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcjbavwxh/bzip2_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-15 [23.4 MB] Fetched 23.4 MB in 0s (163 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpodpz9g9a/gcc-15-x86-64-linux-gnu_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Fetched 59.6 kB in 0s (5110 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnhae309t/python3-sphinx-argparse_0.5.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Fetched 772 kB in 0s (58.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvzpikdhq/autopoint_0.23.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20260223 [158 kB] Fetched 158 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvynrodzq/ca-certificates_20260223_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.30-1 [52.2 kB] Fetched 52.2 kB in 0s (4135 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprolt7fkx/libthai0_0.1.30-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.20 [29.7 kB] Fetched 29.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp784ftph9/tex-common_6.20_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Fetched 19.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptekug80z/libsasl2-modules-db_2.1.28+dfsg1-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Fetched 27.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwc7gcx4a/python3_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptt003zgt/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Fetched 47.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpln2u2c8q/libpkgconf7_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-16+b1 [15.3 kB] Fetched 15.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsgjc9mq7/libijs-0.35_0.35-16+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Fetched 12.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp837_j20b/netbase_6.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxdot4 amd64 14.1.2-1 [21.9 kB] Fetched 21.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo5wego0x/libxdot4_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1n5h4910/libncursesw6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmuparser2v5 amd64 2.3.4-2 [151 kB] Fetched 151 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd0mc4hjm/libmuparser2v5_2.3.4-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b1 [9784 B] Fetched 9784 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp82umbt4g/libkeyutils1_1.6.3-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Fetched 43.8 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpis73f7hl/file_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-9 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc6hsfqrb/libltdl-dev_2.5.4-9_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte3 amd64 3.0.13-2 [451 kB] Fetched 451 kB in 0s (39.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj3fb0ef1/libprrte3_3.0.13-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Fetched 492 kB in 0s (43.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp32nxj08_/libabsl20240722_20240722.0-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcf2cn_sb/libxcb1_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.46-3 [1058 kB] Fetched 1058 kB in 0s (72.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp96rzklxx/binutils-x86-64-linux-gnu_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rdfind amd64 1.6.0-1+b1 [44.7 kB] Fetched 44.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1nqtnwx0/rdfind_1.6.0-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang1-21 amd64 1:21.1.8-5 [7699 kB] Fetched 7699 kB in 0s (118 MB/s) dpkg-name: info: moved 'libclang1-21_1%3a21.1.8-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpob15wsss/libclang1-21_21.1.8-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.87.2-3 [1552 kB] Fetched 1552 kB in 0s (79.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd8a1c238/libglib2.0-0t64_2.87.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxz03vukg/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2 [105 kB] Fetched 105 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzkv2bkhe/libnl-3-dev_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Fetched 75.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps39t58hs/xdg-utils_1.2.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.12-1 [776 kB] Fetched 776 kB in 0s (59.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqf229y3t/python3.13_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-2 [27.2 kB] Fetched 27.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpusv06z64/python3-pluggy_1.6.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2025.20260124-1 [32.8 MB] Fetched 32.8 MB in 0s (76.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3apiqbo4/texlive-latex-extra_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Fetched 68.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt6bnzd28/libuchardet0_0.0.8-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 16-20260308-1 [147 kB] Fetched 147 kB in 0s (14.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvkbud3sw/libquadmath0_16-20260308-1_amd64.deb' Downloading dependency 130 of 466: python3-sphinx-inline-tabs:amd64=2023.4.21-3 Downloading dependency 131 of 466: m4:amd64=1.4.21-1 Downloading dependency 132 of 466: libfreetype6:amd64=2.14.2+dfsg-1 Downloading dependency 133 of 466: libtool:amd64=2.5.4-9 Downloading dependency 134 of 466: cpp-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 135 of 466: libjbig0:amd64=2.1-6.1+b3 Downloading dependency 136 of 466: texlive-fonts-recommended:amd64=2025.20260124-1 Downloading dependency 137 of 466: python3-certifi:amd64=2026.2.25+ds-1 Downloading dependency 138 of 466: libgs10-common:amd64=10.06.0~dfsg-3 Downloading dependency 139 of 466: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 140 of 466: xml-core:amd64=0.19 Downloading dependency 141 of 466: libsemanage2:amd64=3.9-1+b1 Downloading dependency 142 of 466: librdmacm1t64:amd64=61.0-2 Downloading dependency 143 of 466: gcc-15:amd64=15.2.0-15 Downloading dependency 144 of 466: findutils:amd64=4.10.0-3 Downloading dependency 145 of 466: gcc-16-base:amd64=16-20260308-1 Downloading dependency 146 of 466: libaudit-common:amd64=1:4.1.2-1 Downloading dependency 147 of 466: libwebpmux3:amd64=1.5.0-0.1+b1 Downloading dependency 148 of 466: patch:amd64=2.8-2 Downloading dependency 149 of 466: libltdl7:amd64=2.5.4-9 Downloading dependency 150 of 466: x11-common:amd64=1:7.7+26 Downloading dependency 151 of 466: libice6:amd64=2:1.1.1-1+b1 Downloading dependency 152 of 466: libcommons-parent-java:amd64=56-1 Downloading dependency 153 of 466: libevent-dev:amd64=2.1.12-stable-10+b2 Downloading dependency 154 of 466: base-files:amd64=14 Downloading dependency 155 of 466: libcc1-0:amd64=16-20260308-1 Downloading dependency 156 of 466: dh-autoreconf:amd64=22 Downloading dependency 157 of 466: mount:amd64=2.41.3-4 Downloading dependency 158 of 466: libavahi-client3:amd64=0.8-18 Downloading dependency 159 of 466: libmagic-mgc:amd64=1:5.46-5+b1 Downloading dependency 160 of 466: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.1-3 Downloading dependency 161 of 466: libmagic1t64:amd64=1:5.46-5+b1 Downloading dependency 162 of 466: fonts-lmodern:amd64=2.005-1 Downloading dependency 163 of 466: sysvinit-utils:amd64=3.15-6 Downloading dependency 164 of 466: libpam-modules:amd64=1.7.0-5+b1 Downloading dependency 165 of 466: init-system-helpers:amd64=1.69 Downloading dependency 166 of 466: libxapian30:amd64=1.4.31-2 Downloading dependency 167 of 466: libxaw7:amd64=2:1.0.16-1+b1 Downloading dependency 168 of 466: libsvtav1enc2:amd64=2.3.0+dfsg-1 Downloading dependency 169 of 466: python3-jinja2:amd64=3.1.6-1 Downloading dependency 170 of 466: libgfortran-15-dev:amd64=15.2.0-15 Downloading dependency 171 of 466: libcrypt1:amd64=1:4.5.1-1 Downloading dependency 172 of 466: libfabric1:amd64=2.1.0-1.1+b1 Downloading dependency 173 of 466: libpciaccess0:amd64=0.17-3+b4 Downloading dependency 174 of 466: cpp-15:amd64=15.2.0-15 Downloading dependency 175 of 466: libyuv0:amd64=0.0.1922.20260106-1 Downloading dependency 176 of 466: preview-latex-style:amd64=13.2-1.1 Downloading dependency 177 of 466: libpixman-1-0:amd64=0.46.4-1+b1 Downloading dependency 178 of 466: python3-pygments:amd64=2.19.2+dfsg-1 Downloading dependency 179 of 466: build-essential:amd64=12.12 Downloading dependency 180 of 466: libdb5.3t64:amd64=5.3.28+dfsg2-11 Downloading dependency 181 of 466: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 182 of 466: libnl-route-3-200:amd64=3.12.0-2 Downloading dependency 183 of 466: python3-pybind11:amd64=3.0.1-3 Downloading dependency 184 of 466: liblsan0:amd64=16-20260308-1 Downloading dependency 185 of 466: libzzip-0-13t64:amd64=0.13.78+dfsg.1-0.2 Downloading dependency 186 of 466: libcups2t64:amd64=2.4.16-1 Downloading dependency 187 of 466: libimagequant0:amd64=4.4.1-1+b1 Downloading dependency 188 of 466: libcurl4t64:amd64=8.19.0~rc3-1 Downloading dependency 189 of 466: tex-gyre:amd64=20180621-7 Downloading dependency 190 of 466: libatomic1:amd64=16-20260308-1 Downloading dependency 191 of 466: libgssapi-krb5-2:amd64=1.22.1-2 Downloading dependency 192 of 466: liblapack-dev:amd64=3.12.1-7+b1 Downloading dependency 193 of 466: xfonts-utils:amd64=1:7.7+7 Downloading dependency 194 of 466: libkrb5-3:amd64=1.22.1-2 Downloading dependency 195 of 466: cpp-15-x86-64-linux-gnu:amd64=15.2.0-15 Downloading dependency 196 of 466: dh-strip-nondeterminism:amd64=1.15.0-1 Downloading dependency 197 of 466: libpsl5t64:amd64=0.21.2-1.1+b2 Downloading dependency 198 of 466: libxi6:amd64=2:1.8.2-2 Downloading dependency 199 of 466: libprrte-dev:amd64=3.0.13-2 Downloading dependency 200 of 466: libbrotli1:amd64=1.2.0-3 Downloading dependency 201 of 466: libcgraph8:amd64=14.1.2-1 Downloading dependency 202 of 466: libtiff6:amd64=4.7.1-1 Downloading dependency 203 of 466: python3-requests:amd64=2.32.5+dfsg-1 Downloading dependency 204 of 466: openmpi-bin:amd64=5.0.10-1 Downloading dependency 205 of 466: libnuma1:amd64=2.0.19-1+b1 Downloading dependency 206 of 466: texlive-base:amd64=2025.20260124-1 Downloading dependency 207 of 466: libarchive13t64:amd64=3.8.5-1 Downloading dependency 208 of 466: texlive-binaries:amd64=2025.20250727.75242+ds-5+b2 Downloading dependency 209 of 466: libuv1t64:amd64=1.51.0-2+b1 Downloading dependency 210 of 466: python3-markupsafe:amd64=3.0.3-1+b1 Downloading dependency 211 of 466: libamdhip64-6:amd64=6.4.3-5 Downloading dependency 212 of 466: perl:amd64=5.40.1-7 Downloading dependency 213 of 466: gcc-15-base:amd64=15.2.0-15 Downloading dependency 214 of 466: libxt6t64:amd64=1:1.2.1-1.3+b1 Downloading dependency 215 of 466: libpdfbox-java:amd64=1:1.8.16-5 Downloading dependency 216 of 466: xz-utils:amd64=5.8.2-2 Downloading dependency 217 of 466: ocl-icd-libopencl1:amd64=2.3.4-1 Downloading dependency 218 of 466: libtexlua53-5:amd64=2025.20250727.75242+ds-5+b2 Downloading dependency 219 of 466: libevent-core-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 220 of 466: libdav1d7:amd64=1.5.3-1+b1 Downloading dependency 221 of 466: bzip2:amd64=1.0.8-6+b1 Downloading dependency 222 of 466: gcc-15-x86-64-linux-gnu:amd64=15.2.0-15 Downloading dependency 223 of 466: python3-sphinx-argparse:amd64=0.5.2-1 Downloading dependency 224 of 466: autopoint:amd64=0.23.2-1 Downloading dependency 225 of 466: ca-certificates:amd64=20260223 Downloading dependency 226 of 466: libthai0:amd64=0.1.30-1 Downloading dependency 227 of 466: tex-common:amd64=6.20 Downloading dependency 228 of 466: libsasl2-modules-db:amd64=2.1.28+dfsg1-10 Downloading dependency 229 of 466: python3:amd64=3.13.9-3 Downloading dependency 230 of 466: dash:amd64=0.5.12-12 Downloading dependency 231 of 466: libpkgconf7:amd64=2.5.1-4 Downloading dependency 232 of 466: libijs-0.35:amd64=0.35-16+b1 Downloading dependency 233 of 466: netbase:amd64=6.5 Downloading dependency 234 of 466: libxdot4:amd64=14.1.2-1 Downloading dependency 235 of 466: libncursesw6:amd64=6.6+20251231-1 Downloading dependency 236 of 466: libmuparser2v5:amd64=2.3.4-2 Downloading dependency 237 of 466: libkeyutils1:amd64=1.6.3-6+b1 Downloading dependency 238 of 466: file:amd64=1:5.46-5+b1 Downloading dependency 239 of 466: libltdl-dev:amd64=2.5.4-9 Downloading dependency 240 of 466: libprrte3:amd64=3.0.13-2 Downloading dependency 241 of 466: libabsl20240722:amd64=20240722.0-4 Downloading dependency 242 of 466: libxcb1:amd64=1.17.0-2+b2 Downloading dependency 243 of 466: binutils-x86-64-linux-gnu:amd64=2.46-3 Downloading dependency 244 of 466: rdfind:amd64=1.6.0-1+b1 Downloading dependency 245 of 466: libclang1-21:amd64=1:21.1.8-5 Downloading dependency 246 of 466: libglib2.0-0t64:amd64=2.87.2-3 Downloading dependency 247 of 466: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 248 of 466: libnl-3-dev:amd64=3.12.0-2 Downloading dependency 249 of 466: xdg-utils:amd64=1.2.1-2 Downloading dependency 250 of 466: python3.13:amd64=3.13.12-1 Downloading dependency 251 of 466: python3-pluggy:amd64=1.6.0-2 Downloading dependency 252 of 466: texlive-latex-extra:amd64=2025.20260124-1 Downloading dependency 253 of 466: libuchardet0:amd64=0.0.8-2+b1 Downloading dependency 254 of 466: libquadmath0:amd64=16-20260308-1 Downloading dependency 255 of 466: libpython3.13-minimal:amd64=3.13.12-1Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Fetched 866 kB in 0s (64.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2x8_0nm0/libpython3.13-minimal_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mpi-default-bin amd64 1.20 [2720 B] Fetched 2720 B in 0s (229 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsrz4khgb/mpi-default-bin_1.20_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 symlinks amd64 1.4-5+b1 [9692 B] Fetched 9692 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjibvp21j/symlinks_1.4-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.55-1 [288 kB] Fetched 288 kB in 0s (21.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_jeat3qz/libpng16-16t64_1.6.55-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 diffutils amd64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (29.2 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp0i_3f3t_/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b3 [23.4 kB] Fetched 23.4 kB in 0s (0 B/s) dpkg-name: info: moved 'libfontenc1_1%3a1.1.8-1+b3_amd64.deb' to '/srv/rebuilderd/tmp/tmp8aokt_2n/libfontenc1_1.1.8-1+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.2.3-12 [619 kB] Fetched 619 kB in 0s (44.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptq1_f3i8/sphinx-common_8.2.3-12_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-11+b1 [77.0 kB] Fetched 77.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgev06ju1/libgraphite2-3_1.3.14-11+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 libudev1 amd64 260~rc2-1 [132 kB] Fetched 132 kB in 0s (9613 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgjntcm8o/libudev1_260~rc2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.9-3 [10.8 kB] Fetched 10.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmu0ykhxs/libpython3-dev_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.14.3-2 [118 kB] Fetched 118 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpct1humdk/python3-bs4_4.14.3-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Fetched 346 kB in 0s (0 B/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmp_h9ya_b_/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Fetched 1194 kB in 0s (78.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptgl97lyn/groff-base_1.23.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Fetched 185 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4mjgqx2b/libelf1t64_0.194-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzma5 amd64 5.8.2-2 [327 kB] Fetched 327 kB in 0s (31.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfnbcn69y/liblzma5_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuujmrrla/dwz_0.16-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-5 [767 kB] Fetched 767 kB in 0s (54.9 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp7xdxmksb/libclang-common-21-dev_21.1.8-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 libavif16 amd64 1.3.0-1+b2 [137 kB] Fetched 137 kB in 0s (12.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9k126q1i/libavif16_1.3.0-1+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b3 [16.5 kB] Fetched 16.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxuqi5h22/libpaper-utils_2.2.5-0.3+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 libsystemd-shared amd64 260~rc2-1 [2400 kB] Fetched 2400 kB in 0s (116 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqedn84al/libsystemd-shared_260~rc2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfc5tmw70/gzip_1.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2+b1 [49.5 kB] Fetched 49.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmymmoh3a/libdeflate0_1.23-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-2 [1561 kB] Fetched 1561 kB in 0s (90.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2sywt88p/bash_5.3-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b2 [805 kB] Fetched 805 kB in 0s (45.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5q83ul4u/libfftw3-single3_3.3.10-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 16-20260308-1 [2889 kB] Fetched 2889 kB in 0s (123 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsts9p8jq/libasan8_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.2p1-5 [1031 kB] Fetched 1031 kB in 0s (71.5 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.2p1-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp4_ka0ftj/openssh-client_10.2p1-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.41.3-4 [1166 kB] Fetched 1166 kB in 0s (73.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmcnmf0wc/util-linux_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg-dev all 1.23.7 [1318 kB] Fetched 1318 kB in 0s (87.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2qw4h5df/dpkg-dev_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Fetched 932 kB in 0s (63.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk4gub03y/debhelper_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.06.0~dfsg-3 [2909 kB] Fetched 2909 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rgt9yy3/libgs10_10.06.0~dfsg-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.21.0-1 [25.9 kB] Fetched 25.9 kB in 0s (2578 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprrcmy_hc/libngtcp2-crypto-ossl0_1.21.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b3 [25.5 kB] Fetched 25.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzn61xmwn/libpotrace0_1.16-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 openssl amd64 3.5.5-1 [1500 kB] Fetched 1500 kB in 0s (88.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpseqxmmh4/openssl_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b2 [603 kB] Fetched 603 kB in 0s (44.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk2q3icnm/libfftw3-quad3_3.3.10-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.12-3 [1520 kB] Fetched 1520 kB in 0s (88.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpolyj47rr/libgnutls30t64_3.8.12-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b1 [40.4 kB] Fetched 40.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4psg8_us/libbz2-1.0_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.46-3 [282 kB] Fetched 282 kB in 0s (25.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprpuoyzsx/binutils_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (36.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpow480uoj/grep_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libwmflite-0.2-7 amd64 0.2.14-1 [74.1 kB] Fetched 74.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb645p8df/libwmflite-0.2-7_0.2.14-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.06.0~dfsg-3 [149 kB] Fetched 149 kB in 0s (14.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpniyouazg/libgs-common_10.06.0~dfsg-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b4 [56.6 kB] Fetched 56.6 kB in 0s (0 B/s) dpkg-name: info: moved 'libxpm4_1%3a3.5.17-1+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmp27g1vuft/libxpm4_3.5.17-1+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.1 [28.7 kB] Fetched 28.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ekd2rzz/libcbor0.10_0.10.2-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Fetched 8808 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfo34cg5q/libtext-wrapi18n-perl_0.06-10_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 61.0-2 [44.9 kB] Fetched 44.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmfd0zoeb/libibmad5_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-15 [2777 kB] Fetched 2777 kB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn06h0ri9/libstdc++-15-dev_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 2.1.0-2 [7540 B] Fetched 7540 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpupiskh0s/python3-iniconfig_2.1.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.16-1.1 [19.6 kB] Fetched 19.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgqtma4fa/libmunge2_0.5.16-1.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpathplan4 amd64 14.1.2-1 [29.9 kB] Fetched 29.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzq4lg4f4/libpathplan4_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Fetched 211 kB in 0s (16.9 MB/s) dpkg-name: info: moved 'libfontbox-java_1%3a1.8.16-5_all.deb' to '/srv/rebuilderd/tmp/tmpp70eca40/libfontbox-java_1.8.16-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b2 [54.3 kB] Fetched 54.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplsypb7w_/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pybind11-dev all 3.0.1-3 [240 kB] Fetched 240 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptdkp097c/pybind11-dev_3.0.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-9+b1 [918 kB] Fetched 918 kB in 0s (58.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpokr6ajfk/libsqlite3-0_3.46.1-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.17.1-5 [56.1 kB] Fetched 56.1 kB in 0s (5269 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoyhne5aa/fontconfig-config_2.17.1-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.12-1 [2187 kB] Fetched 2187 kB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7avg86d1/libpython3.13_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-roman-numerals all 4.1.0-1 [9196 B] Fetched 9196 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5vh30g8s/python3-roman-numerals_4.1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Fetched 10.8 MB in 0s (133 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0nopql8f/fonts-urw-base35_20200910-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 16-20260308-1 [73.8 kB] Fetched 73.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0w8jv5lv/libgcc-s1_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmuparser-dev amd64 2.3.4-2 [33.3 kB] Fetched 33.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu933n293/libmuparser-dev_2.3.4-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16-20260308-1 [884 kB] Fetched 884 kB in 0s (66.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnzy8wc46/libgfortran5_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b1 [561 kB] Fetched 561 kB in 0s (44.4 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpt9f4_6cx/libgmp10_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.16.0-8 [319 kB] Fetched 319 kB in 0s (25.2 MB/s) dpkg-name: info: moved 'bash-completion_1%3a2.16.0-8_all.deb' to '/srv/rebuilderd/tmp/tmph8v993jl/bash-completion_2.16.0-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Fetched 30.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd0583f3w/openmpi-common_5.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmparro2s3y/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2025.20250727.75242+ds-5+b2 [62.1 kB] Fetched 62.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa2z58t04/libsynctex2_2025.20250727.75242+ds-5+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-18 [113 kB] Fetched 113 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqc3lk74a/libavahi-common-data_0.8-18_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.20.0+ds-4 [938 kB] Fetched 938 kB in 0s (69.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpipmp787y/libucx0_1.20.0+ds-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsemanage-common all 3.9-1 [7888 B] Fetched 7888 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu1hbr95g/libsemanage-common_3.9-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7+b1 [209 kB] Fetched 209 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyzzhhuxe/libblas3_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgvplugin-pango8 amd64 14.1.2-1 [31.6 kB] Fetched 31.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaex23j0w/libgvplugin-pango8_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1+b1 [27.7 kB] Fetched 27.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxrender1_1%3a0.9.12-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpb9xkq1eu/libxrender1_0.9.12-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.57.0-1 [229 kB] Fetched 229 kB in 0s (20.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbaaem021/libpango-1.0-0_1.57.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdpkg-perl all 1.23.7 [669 kB] Fetched 669 kB in 0s (49.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprxx_62_p/libdpkg-perl_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.22.4+dfsg-1 [433 kB] Fetched 433 kB in 0s (38.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3yvdekuh/python3-docutils_0.22.4+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1+b1 [116 kB] Fetched 116 kB in 0s (11.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt52zfv9n/libsharpyuv0_1.5.0-0.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Fetched 19.9 kB in 0s (1622 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8lek_bub/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [58.7 kB] Fetched 58.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp04vndyud/libpangoft2-1.0-0_1.57.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b5 [9532 B] Fetched 9532 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb46w_j0x/libtext-charwidth-perl_0.04-11+b5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b2 [61.3 kB] Fetched 61.3 kB in 0s (6052 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_opl21f5/libevent-openssl-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Fetched 27.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8iyejk1i/python3-minimal_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Fetched 1687 kB in 0s (98.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr7iq2eqs/gettext_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpamxn1qr4/autotools-dev_20240727.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Fetched 81.1 kB in 0s (7254 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpymczuijd/libk5crypto3_1.22.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1 [354 kB] Fetched 354 kB in 0s (30.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg143thru/libtinfo6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b2 [51.0 kB] Fetched 51.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxjdvkd2p/libfftw3-bin_3.3.10-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Fetched 19.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1t6zd51l/libcom-err2_1.47.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Fetched 181 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp53cusa1x/libreadline8t64_8.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-15 [12.8 MB] Fetched 12.8 MB in 0s (161 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqj3gj95z/gfortran-15-x86-64-linux-gnu_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Fetched 10.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1jf04tas/python3-sphinxcontrib.autoprogram_0.1.9-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b1 [308 kB] Fetched 308 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_m41w0wh/libzstd1_1.5.7+dfsg-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 linux-libc-dev all 6.19.6-1 [1942 kB] Fetched 1942 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvqs4tkfb/linux-libc-dev_6.19.6-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgvc7 amd64 14.1.2-1 [376 kB] Fetched 376 kB in 0s (32.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphd1_godz/libgvc7_14.1.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzdi6x6s_/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.14-2+b4 [40.1 kB] Fetched 40.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc8pkyiaz/libjansson4_2.14-2+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-5 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp6s6tzkpp/g++-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.41.3-4 [212 kB] Fetched 212 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxn665jrt/libmount1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Fetched 50.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpx15py_pa/libxext6_1.3.4-1+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15 amd64 15.2.0-15 [26.3 kB] Fetched 26.3 kB in 0s (2426 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa966zca0/g++-15_15.2.0-15_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Fetched 54.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt84b0wbl/base-passwd_3.6.8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 libssl3t64 amd64 3.5.5-1 [2449 kB] Fetched 2449 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpavxnplff/libssl3t64_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte-bin amd64 3.0.13-2 [51.8 kB] Fetched 51.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppos_epn0/libprrte-bin_3.0.13-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Fetched 1679 kB in 0s (91.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkl30qhed/perl-base_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.46-3 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9txiz7wo/libctf-nobfd0_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Fetched 6688 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdjr1qr85/python3-imagesize_1.4.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Fetched 2267 kB in 0s (116 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp161l6htn/python3.13-minimal_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b2 [346 kB] Fetched 346 kB in 0s (28.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp39fxw52/libfftw3-long3_3.3.10-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7+b1 [222 kB] Fetched 222 kB in 0s (21.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpot99foa5/libblas-dev_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpc3 amd64 1.3.1-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvvvah7j5/libmpc3_1.3.1-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.12-1 [1974 kB] Fetched 1974 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpttl6pnlu/libpython3.13-stdlib_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 16-20260308-1 [1136 kB] Fetched 1136 kB in 0s (76.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzqugzwi6/libubsan1_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-13 [2016 kB] Fetched 2016 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1258x4yu/libc6-dev_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b2 [775 kB] Fetched 775 kB in 0s (59.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp57rdu_xa/libfftw3-double3_3.3.10-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-13 [1814 kB] Fetched 1814 kB in 0s (97.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwr8ejdww/libc6_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 61.0-2 [30.2 kB] Fetched 30.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyauio3vx/libibumad3_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librav1e0.8 amd64 0.8.1-7 [978 kB] Fetched 978 kB in 0s (72.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmdlsd8im/librav1e0.8_0.8.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.14-1 [39.6 kB] Fetched 39.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkg_r6sr8/libdatrie1_0.2.14-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-13 [644 kB] Fetched 644 kB in 0s (45.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg18gwxiq/libc-bin_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 passwd amd64 1:4.19.3-1 [1288 kB] Fetched 1288 kB in 0s (74.5 MB/s) dpkg-name: info: moved 'passwd_1%3a4.19.3-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp0ijng94w/passwd_4.19.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1+b1 [8646 kB] Fetched 8646 kB in 0s (155 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfvothoot/libz3-4_4.13.3-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 1.0.0-1 [20.4 kB] Fetched 20.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo9o7_sr4/python3-alabaster_1.0.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6+b1 [2652 B] Fetched 2652 B in 0s (236 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvolb2e8d/architecture-properties_0.2.6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-6 [494 kB] Fetched 494 kB in 0s (40.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu6sz0uiy/autoconf_2.72-6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.21.0-2 [50.4 kB] Fetched 50.4 kB in 0s (4595 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5sr0wso5/libtasn1-6_4.21.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Fetched 116 kB in 0s (8983 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq8_1mqsr/libexpat1_2.7.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.2.3-2 [13.0 MB] Fetched 13.0 MB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpotolwdze/cmake_4.2.3-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.17-1 [163 kB] Fetched 163 kB in 0s (15.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkd8h9ulu/liblcms2-2_2.17-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2 [220 kB] Fetched 220 kB in 0s (18.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_2q4z6f4/libnl-route-3-dev_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.11-1 [41.7 kB] Fetched 41.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdbmakz08/python3-idna_3.11-1_all.deb' Downloading dependency 256 of 466: mpi-default-bin:amd64=1.20 Downloading dependency 257 of 466: symlinks:amd64=1.4-5+b1 Downloading dependency 258 of 466: libpng16-16t64:amd64=1.6.55-1 Downloading dependency 259 of 466: diffutils:amd64=1:3.12-1 Downloading dependency 260 of 466: libfontenc1:amd64=1:1.1.8-1+b3 Downloading dependency 261 of 466: sphinx-common:amd64=8.2.3-12 Downloading dependency 262 of 466: libgraphite2-3:amd64=1.3.14-11+b1 Downloading dependency 263 of 466: libudev1:amd64=260~rc2-1 Downloading dependency 264 of 466: libpython3-dev:amd64=3.13.9-3 Downloading dependency 265 of 466: python3-bs4:amd64=4.14.3-2 Downloading dependency 266 of 466: libx11-data:amd64=2:1.8.13-1 Downloading dependency 267 of 466: groff-base:amd64=1.23.0-10 Downloading dependency 268 of 466: libelf1t64:amd64=0.194-1 Downloading dependency 269 of 466: liblzma5:amd64=5.8.2-2 Downloading dependency 270 of 466: dwz:amd64=0.16-2 Downloading dependency 271 of 466: libclang-common-21-dev:amd64=1:21.1.8-5 Downloading dependency 272 of 466: libavif16:amd64=1.3.0-1+b2 Downloading dependency 273 of 466: libpaper-utils:amd64=2.2.5-0.3+b3 Downloading dependency 274 of 466: libsystemd-shared:amd64=260~rc2-1 Downloading dependency 275 of 466: gzip:amd64=1.13-1 Downloading dependency 276 of 466: libdeflate0:amd64=1.23-2+b1 Downloading dependency 277 of 466: bash:amd64=5.3-2 Downloading dependency 278 of 466: libfftw3-single3:amd64=3.3.10-2+b2 Downloading dependency 279 of 466: libasan8:amd64=16-20260308-1 Downloading dependency 280 of 466: openssh-client:amd64=1:10.2p1-5 Downloading dependency 281 of 466: util-linux:amd64=2.41.3-4 Downloading dependency 282 of 466: dpkg-dev:amd64=1.23.7 Downloading dependency 283 of 466: debhelper:amd64=13.31 Downloading dependency 284 of 466: libgs10:amd64=10.06.0~dfsg-3 Downloading dependency 285 of 466: libngtcp2-crypto-ossl0:amd64=1.21.0-1 Downloading dependency 286 of 466: libpotrace0:amd64=1.16-2+b3 Downloading dependency 287 of 466: openssl:amd64=3.5.5-1 Downloading dependency 288 of 466: libfftw3-quad3:amd64=3.3.10-2+b2 Downloading dependency 289 of 466: libgnutls30t64:amd64=3.8.12-3 Downloading dependency 290 of 466: libbz2-1.0:amd64=1.0.8-6+b1 Downloading dependency 291 of 466: binutils:amd64=2.46-3 Downloading dependency 292 of 466: grep:amd64=3.12-1 Downloading dependency 293 of 466: libwmflite-0.2-7:amd64=0.2.14-1 Downloading dependency 294 of 466: libgs-common:amd64=10.06.0~dfsg-3 Downloading dependency 295 of 466: libxpm4:amd64=1:3.5.17-1+b4 Downloading dependency 296 of 466: libcbor0.10:amd64=0.10.2-2.1 Downloading dependency 297 of 466: libtext-wrapi18n-perl:amd64=0.06-10 Downloading dependency 298 of 466: libibmad5:amd64=61.0-2 Downloading dependency 299 of 466: libstdc++-15-dev:amd64=15.2.0-15 Downloading dependency 300 of 466: python3-iniconfig:amd64=2.1.0-2 Downloading dependency 301 of 466: libmunge2:amd64=0.5.16-1.1 Downloading dependency 302 of 466: libpathplan4:amd64=14.1.2-1 Downloading dependency 303 of 466: libfontbox-java:amd64=1:1.8.16-5 Downloading dependency 304 of 466: libevent-pthreads-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 305 of 466: pybind11-dev:amd64=3.0.1-3 Downloading dependency 306 of 466: libsqlite3-0:amd64=3.46.1-9+b1 Downloading dependency 307 of 466: fontconfig-config:amd64=2.17.1-5 Downloading dependency 308 of 466: libpython3.13:amd64=3.13.12-1 Downloading dependency 309 of 466: python3-roman-numerals:amd64=4.1.0-1 Downloading dependency 310 of 466: fonts-urw-base35:amd64=20200910-8 Downloading dependency 311 of 466: libgcc-s1:amd64=16-20260308-1 Downloading dependency 312 of 466: libmuparser-dev:amd64=2.3.4-2 Downloading dependency 313 of 466: libgfortran5:amd64=16-20260308-1 Downloading dependency 314 of 466: libgmp10:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 315 of 466: bash-completion:amd64=1:2.16.0-8 Downloading dependency 316 of 466: openmpi-common:amd64=5.0.10-1 Downloading dependency 317 of 466: sensible-utils:amd64=0.0.26 Downloading dependency 318 of 466: libsynctex2:amd64=2025.20250727.75242+ds-5+b2 Downloading dependency 319 of 466: libavahi-common-data:amd64=0.8-18 Downloading dependency 320 of 466: libucx0:amd64=1.20.0+ds-4 Downloading dependency 321 of 466: libsemanage-common:amd64=3.9-1 Downloading dependency 322 of 466: libblas3:amd64=3.12.1-7+b1 Downloading dependency 323 of 466: libgvplugin-pango8:amd64=14.1.2-1 Downloading dependency 324 of 466: libxrender1:amd64=1:0.9.12-1+b1 Downloading dependency 325 of 466: libpango-1.0-0:amd64=1.57.0-1 Downloading dependency 326 of 466: libdpkg-perl:amd64=1.23.7 Downloading dependency 327 of 466: python3-docutils:amd64=0.22.4+dfsg-1 Downloading dependency 328 of 466: libsharpyuv0:amd64=1.5.0-0.1+b1 Downloading dependency 329 of 466: libfile-stripnondeterminism-perl:amd64=1.15.0-1 Downloading dependency 330 of 466: libpangoft2-1.0-0:amd64=1.57.0-1 Downloading dependency 331 of 466: libtext-charwidth-perl:amd64=0.04-11+b5 Downloading dependency 332 of 466: libevent-openssl-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 333 of 466: python3-minimal:amd64=3.13.9-3 Downloading dependency 334 of 466: gettext:amd64=0.23.2-1 Downloading dependency 335 of 466: autotools-dev:amd64=20240727.1 Downloading dependency 336 of 466: libk5crypto3:amd64=1.22.1-2 Downloading dependency 337 of 466: libtinfo6:amd64=6.6+20251231-1 Downloading dependency 338 of 466: libfftw3-bin:amd64=3.3.10-2+b2 Downloading dependency 339 of 466: libcom-err2:amd64=1.47.4-1 Downloading dependency 340 of 466: libreadline8t64:amd64=8.3-4 Downloading dependency 341 of 466: gfortran-15-x86-64-linux-gnu:amd64=15.2.0-15 Downloading dependency 342 of 466: python3-sphinxcontrib.autoprogram:amd64=0.1.9-1 Downloading dependency 343 of 466: libzstd1:amd64=1.5.7+dfsg-3+b1 Downloading dependency 344 of 466: linux-libc-dev:amd64=6.19.6-1 Downloading dependency 345 of 466: libgvc7:amd64=14.1.2-1 Downloading dependency 346 of 466: hostname:amd64=3.25 Downloading dependency 347 of 466: libjansson4:amd64=2.14-2+b4 Downloading dependency 348 of 466: g++-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 349 of 466: libmount1:amd64=2.41.3-4 Downloading dependency 350 of 466: libxext6:amd64=2:1.3.4-1+b4 Downloading dependency 351 of 466: g++-15:amd64=15.2.0-15 Downloading dependency 352 of 466: base-passwd:amd64=3.6.8 Downloading dependency 353 of 466: libssl3t64:amd64=3.5.5-1 Downloading dependency 354 of 466: libprrte-bin:amd64=3.0.13-2 Downloading dependency 355 of 466: perl-base:amd64=5.40.1-7 Downloading dependency 356 of 466: libctf-nobfd0:amd64=2.46-3 Downloading dependency 357 of 466: python3-imagesize:amd64=1.4.1-1 Downloading dependency 358 of 466: python3.13-minimal:amd64=3.13.12-1 Downloading dependency 359 of 466: libfftw3-long3:amd64=3.3.10-2+b2 Downloading dependency 360 of 466: libblas-dev:amd64=3.12.1-7+b1 Downloading dependency 361 of 466: libmpc3:amd64=1.3.1-2+b1 Downloading dependency 362 of 466: libpython3.13-stdlib:amd64=3.13.12-1 Downloading dependency 363 of 466: libubsan1:amd64=16-20260308-1 Downloading dependency 364 of 466: libc6-dev:amd64=2.42-13 Downloading dependency 365 of 466: libfftw3-double3:amd64=3.3.10-2+b2 Downloading dependency 366 of 466: libc6:amd64=2.42-13 Downloading dependency 367 of 466: libibumad3:amd64=61.0-2 Downloading dependency 368 of 466: librav1e0.8:amd64=0.8.1-7 Downloading dependency 369 of 466: libdatrie1:amd64=0.2.14-1 Downloading dependency 370 of 466: libc-bin:amd64=2.42-13 Downloading dependency 371 of 466: passwd:amd64=1:4.19.3-1 Downloading dependency 372 of 466: libz3-4:amd64=4.13.3-1+b1 Downloading dependency 373 of 466: python3-alabaster:amd64=1.0.0-1 Downloading dependency 374 of 466: architecture-properties:amd64=0.2.6+b1 Downloading dependency 375 of 466: autoconf:amd64=2.72-6 Downloading dependency 376 of 466: libtasn1-6:amd64=4.21.0-2 Downloading dependency 377 of 466: libexpat1:amd64=2.7.4-1 Downloading dependency 378 of 466: cmake:amd64=4.2.3-2 Downloading dependency 379 of 466: liblcms2-2:amd64=2.17-1 Downloading dependency 380 of 466: libnl-route-3-dev:amd64=3.12.0-2 Downloading dependency 381 of 466: python3-idna:amd64=3.11-1 Downloading dependency 382 of 466: libevent-2.1-7t64:amd64=2.1.12-stable-10+b2Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Fetched 184 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvnyhbshe/libevent-2.1-7t64_2.1.12-stable-10+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 12.3.2-2+b2 [513 kB] Fetched 513 kB in 0s (43.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprr_o82n5/libharfbuzz0b_12.3.2-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-2 [92.5 kB] Fetched 92.5 kB in 0s (6795 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9mh0i20m/python3-typing-extensions_4.15.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 login.defs all 1:4.19.3-1 [211 kB] Fetched 211 kB in 0s (20.9 MB/s) dpkg-name: info: moved 'login.defs_1%3a4.19.3-1_all.deb' to '/srv/rebuilderd/tmp/tmp_mkveozo/login.defs_4.19.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Fetched 577 kB in 0s (45.2 MB/s) dpkg-name: info: moved 'xfonts-encodings_1%3a1.0.4-2.2_all.deb' to '/srv/rebuilderd/tmp/tmptoknkhn4/xfonts-encodings_1.0.4-2.2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20251231-1 [445 kB] Fetched 445 kB in 0s (31.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp09hq9r1j/ncurses-bin_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Fetched 42.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpreji799w/libpipeline1_1.5.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 16-20260308-1 [26.9 kB] Fetched 26.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcpw24142/libitm1_16-20260308-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-12 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5nx0vtly/libjs-sphinxdoc_8.2.3-12_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b1 [20.8 kB] Fetched 20.8 kB in 0s (1816 kB/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp73a9z68q/libxau6_1.0.11-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Fetched 68.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppa4llbs1/libcommons-logging-java_1.3.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Fetched 75.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl6_hx35g/libdebhelper-perl_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.13.0-2 [23.5 kB] Fetched 23.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy4or3ffr/libhwloc-plugins_2.13.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2 [62.2 kB] Fetched 62.2 kB in 0s (5258 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb5d232d3/libnl-3-200_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-5 [26.7 kB] Fetched 26.7 kB in 0s (2296 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptae7l8zq/libfribidi0_1.0.16-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Fetched 877 kB in 0s (64.3 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmpg7msg_8_/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgvpr2 amd64 14.1.2-1 [125 kB] Fetched 125 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjhwwgzoe/libgvpr2_14.1.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 python3-packaging all 25.0-2 [56.7 kB] Fetched 56.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvo5cm5s4/python3-packaging_25.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.13+ds-1 [369 kB] Fetched 369 kB in 0s (33.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9s2_yv7a/libteckit0_2.5.13+ds-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-4 [180 kB] Fetched 180 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplekgm8u3/libdbus-1-3_1.16.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4+b1 [110 kB] Fetched 110 kB in 0s (10.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7iewhx2l/libidn2-0_2.3.8-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Fetched 43.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaim2gi1c/python3-defusedxml_0.7.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.3-4 [98.9 kB] Fetched 98.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp22mcg99l/bsdextrautils_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (24.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp50sq_vua/libpam-runtime_1.7.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.4.2-4 [24.1 MB] Fetched 24.1 MB in 0s (73.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps9mfelil/python3-networkx_3.4.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2025.20260124-1 [1340 kB] Fetched 1340 kB in 0s (69.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu8arvc2s/texlive-latex-base_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1+b1 [78.9 kB] Fetched 78.9 kB in 0s (5476 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3q1xw4ng/libgdbm6t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.41.3-4 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4617psbc/libsmartcols1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Fetched 319 kB in 0s (27.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxyrsdjfb/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1+b1 [336 kB] Fetched 336 kB in 0s (31.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl1p2mtrv/libwebp7_1.5.0-0.1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [24.5 kB] Fetched 24.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwwzzl2md/libdrm-amdgpu1_2.4.131-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sphinx-basic-ng all 1.0.0~beta2-1 [13.0 kB] Fetched 13.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ndaefi_/sphinx-basic-ng_1.0.0~beta2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.21.2-3 [20.6 kB] Fetched 20.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfkkr5xfa/libheif-plugin-dav1d_1.21.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2025.20260124-1 [23.6 MB] Fetched 23.6 MB in 0s (83.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbjl_4zkz/texlive-pictures_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5+b1 [49.8 kB] Fetched 49.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq5boh4bg/libpam-modules-bin_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.13.1-2 [1906 kB] Fetched 1906 kB in 0s (107 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqear_dtv/libaom3_3.13.1-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.26.2-2 [470 kB] Fetched 470 kB in 0s (34.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4lz5tt8f/libp11-kit0_0.26.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Fetched 14.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2wc26qbu/libxnvctrl0_535.171.04-1+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 make amd64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (27.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0cmqkp2a/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [195 kB] Fetched 195 kB in 0s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplb88py0a/libldap2_2.6.10+dfsg-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.41.3-4 [174 kB] Fetched 174 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfc7hds0u/libblkid1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Fetched 10.9 kB in 0s (1081 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5bqwac14/sgml-base_1.31+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20251016-1 [93.6 kB] Fetched 93.6 kB in 0s (7079 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpephsbn9z/libedit2_3.1-20251016-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Fetched 87.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn0zfxpqh/libjson-perl_4.10000-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1+b1 [298 kB] Fetched 298 kB in 0s (26.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplhbqtweh/libpcre2-8-0_10.46-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Fetched 35.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptcfwb29l/pkgconf-bin_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-1+b1 [663 kB] Fetched 663 kB in 0s (34.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd2b8qnmp/libisl23_0.27-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 lsb-release all 12.1-2 [6072 B] Fetched 6072 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5scjfvli/lsb-release_12.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Fetched 30.8 kB in 0s (2879 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3jtvm91l/media-types_14.0.0_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.4-1 [169 kB] Fetched 169 kB in 0s (15.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4oesp19r/libexpat1-dev_2.7.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.17.1-5 [191 kB] Fetched 191 kB in 0s (15.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm1xk0867/fontconfig_2.17.1-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Fetched 245 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy7ecy3of/gettext-base_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-4 [59.4 kB] Fetched 59.4 kB in 0s (0 B/s) dpkg-name: info: moved 'libxmu6_2%3a1.1.3-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpe9p956e5/libxmu6_1.1.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 61.0-2 [381 kB] Fetched 381 kB in 0s (23.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpltaq23cx/ibverbs-providers_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3+b1 [60.7 kB] Fetched 60.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphcfnmjwd/librtmp1_2.4+20151223.gitfa8646d.1-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libclang-cpp21 amd64 1:21.1.8-5 [12.8 MB] Fetched 12.8 MB in 0s (118 MB/s) dpkg-name: info: moved 'libclang-cpp21_1%3a21.1.8-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp49y0hike/libclang-cpp21_21.1.8-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Fetched 63.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp023x3atr/python3-snowballstemmer_3.0.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 systemd amd64 260~rc2-1 [3287 kB] Fetched 3287 kB in 0s (111 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsj77408e/systemd_260~rc2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 61.0-2 [64.2 kB] Fetched 64.2 kB in 0s (4102 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcs1pgzuf/libibverbs1_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Fetched 336 kB in 0s (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjp6ecc06/libhogweed6t64_3.10.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b4 [65.3 kB] Fetched 65.3 kB in 0s (6467 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkt4y2xdi/libjbig2dec0_0.20-1+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.9-3 [26.0 kB] Fetched 26.0 kB in 0s (2552 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqtmqfy8x/python3-dev_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.1-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdbxtgrue/libfuse3-4_3.18.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.131-1 [9168 B] Fetched 9168 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwcxt_vhx/libdrm-common_2.4.131-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libicu78 amd64 78.2-2 [10.0 MB] Fetched 10.0 MB in 0s (166 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphn7cx87d/libicu78_78.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Fetched 67.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwmhh5iyf/libnghttp3-9_1.15.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 python3-mpi4py amd64 4.1.1-1+b1 [1144 kB] Fetched 1144 kB in 0s (69.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7tiyiulm/python3-mpi4py_4.1.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.21.2-3 [18.0 kB] Fetched 18.0 kB in 0s (1784 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvipflznm/libheif-plugin-libde265_1.21.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-13 [61.5 kB] Fetched 61.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpobl7c7ud/libc-dev-bin_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (19.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw1fc4_hs/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debianutils amd64 5.23.2 [92.4 kB] Fetched 92.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8afhv1y/debianutils_5.23.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b2 [36.2 kB] Fetched 36.2 kB in 0s (3147 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq1pz2429/libmd0_1.1.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b2 [115 kB] Fetched 115 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3g5xbt_9/libxcb-render0_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.46-3 [2632 kB] Fetched 2632 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4gf7vqps/binutils-common_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfr6 amd64 4.2.2-2+b1 [729 kB] Fetched 729 kB in 0s (58.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkv3xr3lr/libmpfr6_4.2.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (4747 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo9hma2bx/libseccomp2_2.6.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.13.0-2 [258 kB] Fetched 258 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph8oyio5l/libhwloc-dev_2.13.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Fetched 3012 kB in 0s (113 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplmsdwh35/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.15.0+ds1-1+b1 [5544 kB] Fetched 5544 kB in 0s (143 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6knmlexs/doxygen_1.15.0+ds1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjxl0.11 amd64 0.11.1-6 [1165 kB] Fetched 1165 kB in 0s (60.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcnzlc3m0/libjxl0.11_0.11.1-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.10-1 [2018 kB] Fetched 2018 kB in 0s (99.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsap0syat/libopenmpi40_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-2 [117 kB] Fetched 117 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph3oy21d7/python3-babel_2.17.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260310T023034Z unstable/main amd64 ucf all 3.0052 [43.3 kB] Fetched 43.3 kB in 0s (3787 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjenpmjrz/ucf_3.0052_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-5 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpkl16fgbw/g++_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3 [673 kB] Fetched 673 kB in 0s (39.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn3d4bgb4/libpmix2t64_6.0.0+really5.0.9-3_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-buildpackage: info: host architecture amd64 dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmppcd1kks8/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q 127.0.0.1 - - [14/Mar/2026 05:50:38] code 404, message File not found 127.0.0.1 - - [14/Mar/2026 05:50:38] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:35911 ./ InRelease 127.0.0.1 - - [14/Mar/2026 05:50:38] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:35911 ./ Release [462 B] 127.0.0.1 - - [14/Mar/2026 05:50:38] code 404, message File not found 127.0.0.1 - - [14/Mar/2026 05:50:38] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:35911 ./ Release.gpg 127.0.0.1 - - [14/Mar/2026 05:50:38] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:35911 ./ Packages [705 kB] Fetched 706 kB in 0s (20.0 MB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./gcc-16-base_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libc-gconv-modules-extra_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libc6_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libgcc-s1_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./mawk_1.3.4.20260302-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./base-files_14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libtinfo6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./bash_5.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libacl1_2.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libattr1_2.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libpcre2-8-0_10.46-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libselinux1_3.9-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libzstd1_1.5.7%2bdfsg-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libssl3t64_3.5.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./openssl-provider-legacy_3.5.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libsystemd0_260%7erc2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./coreutils_9.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./dash_0.5.12-12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./diffutils_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libbz2-1.0_1.0.8-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./liblzma5_5.8.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libmd0_1.1.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./tar_1.35%2bdfsg-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./dpkg_1.23.7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./findutils_4.10.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./grep_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./gzip_1.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./hostname_3.25_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./ncurses-bin_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libcrypt1_4.5.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./perl-base_5.40.1-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libaudit-common_4.1.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libcap-ng0_0.9.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libaudit1_4.1.2-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libdb5.3t64_5.3.28%2bdfsg2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./debconf_1.5.92_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libpam0g_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libpam-modules-bin_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libpam-modules_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libpam-runtime_1.7.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libblkid1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libmount1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libsmartcols1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libudev1_260%7erc2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libuuid1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./util-linux_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libdebconfclient0_0.282%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./libc-bin_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./ncurses-base_6.6%2b20251231-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:39] "GET /./sysvinit-utils_3.15-6_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q 127.0.0.1 - - [14/Mar/2026 05:50:40] code 404, message File not found 127.0.0.1 - - [14/Mar/2026 05:50:40] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:35911 ./ InRelease 127.0.0.1 - - [14/Mar/2026 05:50:40] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:35911 ./ Release 127.0.0.1 - - [14/Mar/2026 05:50:40] code 404, message File not found 127.0.0.1 - - [14/Mar/2026 05:50:40] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:35911 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./mount_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libsystemd-shared_260%7erc2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./systemd_260%7erc2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libexpat1_2.7.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./poppler-data_0.4.12-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libpython3.13-minimal_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./python3.13-minimal_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./python3-minimal_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./media-types_14.0.0_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./netbase_6.5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./tzdata_2026a-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libffi8_3.5.2-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libncursesw6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./readline-common_8.3-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libreadline8t64_8.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libsqlite3-0_3.46.1-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libpython3.13-stdlib_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./python3.13_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libpython3-stdlib_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./python3_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./python3-numpy-dev_2.3.5%2bds-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libblas3_3.12.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libgfortran5_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./liblapack3_3.12.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libstdc%2b%2b6_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./python3-numpy_2.3.5%2bds-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libtext-charwidth-perl_0.04-11%2bb5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libtext-wrapi18n-perl_0.06-10_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./login.defs_4.19.3-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libbsd0_0.12.2-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libsemanage-common_3.9-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libsepol2_3.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libsemanage2_3.9-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./passwd_4.19.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./sensible-utils_0.0.26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./adduser_3.154_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libuchardet0_0.0.8-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./groff-base_1.23.0-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./bsdextrautils_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libgdbm6t64_1.26-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libpipeline1_1.5.8-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libseccomp2_2.6.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./man-db_2.13.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libproc2-0_4.0.4-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./procps_4.0.4-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./bash-completion_2.16.0-8_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./bzip2_1.0.8-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./openssl_3.5.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./ca-certificates_20260223_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libmagic-mgc_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libmagic1t64_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./file_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./gettext-base_0.23.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libedit2_3.1-20251016-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libcbor0.10_0.10.2-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libfido2-1_1.16.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libkrb5support0_1.22.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libcom-err2_1.47.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libk5crypto3_1.22.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libkeyutils1_1.6.3-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libkrb5-3_1.22.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libgssapi-krb5-2_1.22.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./openssh-client_10.2p1-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./perl-modules-5.40_5.40.1-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libgdbm-compat4t64_1.26-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./libperl5.40_5.40.1-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./perl_5.40.1-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./ucf_3.0052_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./xz-utils_5.8.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./architecture-properties_0.2.6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:47] "GET /./m4_1.4.21-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./autoconf_2.72-6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./autotools-dev_20240727.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./automake_1.18.1-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./autopoint_0.23.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libsframe3_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./binutils-common_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libbinutils_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libgprofng0_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libctf-nobfd0_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libctf0_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libjansson4_2.14-2%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./binutils-x86-64-linux-gnu_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./binutils_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libc-dev-bin_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./linux-libc-dev_6.19.6-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./rpcsvc-proto_1.4.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libc6-dev_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./gcc-15-base_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libisl23_0.27-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libmpfr6_4.2.2-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libmpc3_1.3.1-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./cpp-15-x86-64-linux-gnu_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./cpp-15_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./cpp_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libcc1-0_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libgomp1_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libitm1_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libatomic1_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libasan8_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./liblsan0_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libtsan2_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libubsan1_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libhwasan0_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libquadmath0_16-20260308-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libgcc-15-dev_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./gcc-15-x86-64-linux-gnu_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./gcc-15_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./gcc-x86-64-linux-gnu_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./gcc_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libstdc%2b%2b-15-dev_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./g%2b%2b-15-x86-64-linux-gnu_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./g%2b%2b-15_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./g%2b%2b-x86-64-linux-gnu_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./g%2b%2b_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./make_4.4.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:48] "GET /./libdpkg-perl_1.23.7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./patch_2.8-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./dpkg-dev_1.23.7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./build-essential_12.12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./cmake-data_4.2.3-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libxxhash0_0.8.3-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./liblz4-1_1.10.0-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libnettle8t64_3.10.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libxml2-16_2.15.1%2bdfsg-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libarchive13t64_3.8.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libnghttp3-9_1.15.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libngtcp2-16_1.21.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libbrotli1_1.2.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libunistring5_1.4.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libidn2-0_2.3.8-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libsasl2-modules-db_2.1.28%2bdfsg1-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libsasl2-2_2.1.28%2bdfsg1-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libldap2_2.6.10%2bdfsg-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libnghttp2-14_1.68.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libngtcp2-crypto-ossl0_1.21.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libpsl5t64_0.21.2-1.1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libhogweed6t64_3.10.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libp11-kit0_0.26.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libtasn1-6_4.21.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libgnutls30t64_3.8.12-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./librtmp1_2.4%2b20151223.gitfa8646d.1-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libssh2-1t64_1.11.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libcurl4t64_8.19.0%7erc3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libjsoncpp26_1.9.6-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./librhash1_1.4.6-1.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libuv1t64_1.51.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./cmake_4.2.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libdebhelper-perl_13.31_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libtool_2.5.4-9_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./dh-autoreconf_22_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libarchive-zip-perl_1.68-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libfile-stripnondeterminism-perl_1.15.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./dh-strip-nondeterminism_1.15.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libelf1t64_0.194-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./dwz_0.16-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./gettext_0.23.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./intltool-debian_0.35.0%2b20060710.6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./po-debconf_1.0.22_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./debhelper_13.31_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libpaper2_2.2.5-0.3%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libde265-0_1.0.16-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-defusedxml_0.7.1-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libjs-sphinxdoc_8.2.3-12_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libjson-perl_4.10000-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./sphinx-common_8.2.3-12_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-alabaster_1.0.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python-babel-localedata_2.17.0-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-babel_2.17.0-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./sgml-base_1.31%2bnmu1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./xml-core_0.19_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./docutils-common_0.22.4%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-roman-numerals_4.1.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-docutils_0.22.4%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-imagesize_1.4.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-markupsafe_3.0.3-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-jinja2_3.1.6-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-packaging_25.0-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-pygments_2.19.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-certifi_2026.2.25%2bds-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-charset-normalizer_3.4.4-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-idna_3.11-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-urllib3_2.6.3-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-chardet_5.2.0%2bdfsg-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-requests_2.32.5%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-snowballstemmer_3.0.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-sphinx_8.2.3-12_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./python3-sphinx-copybutton_0.5.2-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libdrm-common_2.4.131-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./libdrm2_2.4.131-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:49] "GET /./liblerc4_4.0.0%2bds-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libnuma1_2.0.19-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libnuma-dev_2.0.19-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./python3-accessible-pygments_0.0.5-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfontenc1_1.1.8-1%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libpng16-16t64_1.6.55-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfreetype6_2.14.2%2bdfsg-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./x11-common_7.7%2b26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./xfonts-encodings_1.0.4-2.2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./xfonts-utils_7.7%2b7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./fonts-urw-base35_20200910-8_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgs-common_10.06.0%7edfsg-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgs10-common_10.06.0%7edfsg-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libavahi-common-data_0.8-18_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libavahi-common3_0.8-18_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libdbus-1-3_1.16.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libavahi-client3_0.8-18_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libcups2t64_2.4.16-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./fontconfig-config_2.17.1-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfontconfig1_2.17.1-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libidn12_1.43-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libijs-0.35_0.35-16%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libjbig2dec0_0.20-1%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libjpeg62-turbo_2.1.5-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./liblcms2-2_2.17-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libopenjp2-7_2.5.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libdeflate0_1.23-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libjbig0_2.1-6.1%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libsharpyuv0_1.5.0-0.1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libwebp7_1.5.0-0.1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libtiff6_4.7.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxau6_1.0.11-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxdmcp6_1.1.5-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxcb1_1.17.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libx11-data_1.8.13-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libx11-6_1.8.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libice6_1.1.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libsm6_1.2.6-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxt6t64_1.2.1-1.3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgs10_10.06.0%7edfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./ghostscript_10.06.0%7edfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libhwy1t64_1.3.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libmpfi0_1.5.4%2bds-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libcdt6_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libcgraph8_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libltdl7_2.5.4-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libpathplan4_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxdot4_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgvc7_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgvpr2_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libpixman-1-0_0.46.4-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxcb-render0_1.17.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxcb-shm0_1.17.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxext6_1.3.4-1%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxrender1_0.9.12-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libcairo2_1.18.4-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libaom3_3.13.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libdav1d7_1.5.3-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libabsl20240722_20240722.0-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgav1-2_0.20.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./librav1e0.8_0.8.1-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libsvtav1enc2_2.3.0%2bdfsg-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libyuv0_0.0.1922.20260106-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libavif16_1.3.0-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libheif-plugin-libde265_1.21.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libheif-plugin-dav1d_1.21.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libheif1_1.21.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libimagequant0_4.4.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libxpm4_3.5.17-1%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgd3_2.3.3-13%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgvplugin-gd8_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libglib2.0-0t64_2.87.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./fontconfig_2.17.1-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfribidi0_1.0.16-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgraphite2-3_1.3.14-11%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libharfbuzz0b_12.3.2-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libthai-data_0.1.30-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libdatrie1_0.2.14-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libthai0_0.1.30-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libpango-1.0-0_1.57.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libpangoft2-1.0-0_1.57.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libpangocairo-1.0-0_1.57.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgvplugin-pango8_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./graphviz_14.1.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libpkgconf7_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./pkgconf-bin_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./pkgconf_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./python3-iniconfig_2.1.0-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./python3-pluggy_1.6.0-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./python3-pytest_9.0.2-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libevent-core-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libevent-extra-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libboost1.90-dev_1.90.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgfortran-15-dev_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./gfortran-15-x86-64-linux-gnu_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./gfortran-15_15.2.0-15_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./dh-python_7.20260125_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./python3-soupsieve_2.8.3-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./python3-typing-extensions_4.15.0-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./python3-bs4_4.14.3-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./sphinx-basic-ng_1.0.0%7ebeta2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./furo_2025.12.19%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfftw3-double3_3.3.10-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfftw3-long3_3.3.10-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfftw3-quad3_3.3.10-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfftw3-single3_3.3.10-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfftw3-bin_3.3.10-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libfftw3-dev_3.3.10-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libjxl0.11_0.11.1-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libwebpmux3_1.5.0-0.1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libwmflite-0.2-7_0.2.14-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libgraphicsmagick-q16-3t64_1.4%2breally1.3.46-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./graphicsmagick_1.4%2breally1.3.46-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libz3-4_4.13.3-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:50] "GET /./libllvm21_21.1.8-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libevent-pthreads-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libnl-3-200_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libnl-route-3-200_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libibverbs1_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./ibverbs-providers_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libpsm2-2_11.2.185-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./librdmacm1t64_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libfabric1_2.1.0-1.1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libhwloc15_2.13.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libmunge2_0.5.16-1.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libpciaccess0_0.17-3%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libxnvctrl0_535.171.04-1%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libze1_1.28.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./ocl-icd-libopencl1_2.3.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libhwloc-plugins_2.13.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libpmix2t64_6.0.0%2breally5.0.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libclang-common-21-dev_21.1.8-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libamd-comgr3_7.0.2%2bdfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libdrm-amdgpu1_2.4.131-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libhsa-runtime64-1_6.4.3%2bdfsg-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libamdhip64-6_6.4.3-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libfuse3-4_3.18.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libibumad3_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libibmad5_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libucx0_1.20.0%2bds-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libucc1_1.7.0%7erc1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libopenmpi40_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./openmpi-common_5.0.10-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libnl-3-dev_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libnl-route-3-dev_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:51] "GET /./libibverbs-dev_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libprrte3_3.0.13-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libjs-jquery_3.7.1%2bdfsg%2b%7e3.5.33-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libprrte-dev_3.0.13-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libltdl-dev_2.5.4-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libhwloc-dev_2.13.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libevent-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libevent-openssl-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libevent-dev_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libjs-jquery-ui_1.13.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libprrte-bin_3.0.13-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./openmpi-bin_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libopenmpi-dev_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./mpi-default-dev_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./mscgen_0.20-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libfmt10_10.1.1%2bds1-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libkpathsea6_2025.20250727.75242%2bds-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./tex-common_6.20_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libpaper-utils_2.2.5-0.3%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libptexenc1_2025.20250727.75242%2bds-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libsynctex2_2025.20250727.75242%2bds-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libtexlua53-5_2025.20250727.75242%2bds-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./t1utils_1.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libicu78_78.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libpotrace0_1.16-2%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libteckit0_2.5.13%2bds-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libxmu6_1.1.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libxaw7_1.0.16-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libxi6_1.8.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libzzip-0-13t64_0.13.78%2bdfsg.1-0.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./texlive-binaries_2025.20250727.75242%2bds-5%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./xdg-utils_1.2.1-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./texlive-base_2025.20260124-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./fonts-lmodern_2.005-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./texlive-latex-base_2025.20260124-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./texlive-latex-recommended_2025.20260124-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libboost-dev_1.90.0.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libpython3.13_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libexpat1-dev_2.7.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libpython3.13-dev_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./python3.13-dev_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libspdlog1.15_1.15.3%2bds-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libapache-pom-java_33-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./python3-sphinx-inline-tabs_2023.4.21-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./texlive-fonts-recommended_2025.20260124-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libcommons-parent-java_56-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libxapian30_1.4.31-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./preview-latex-style_13.2-1.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./libpython3-dev_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./pybind11-dev_3.0.1-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./python3-pybind11_3.0.1-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:52] "GET /./tex-gyre_20180621-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./libblas-dev_3.12.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./liblapack-dev_3.12.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./libfontbox-java_1.8.16-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./libpdfbox-java_1.8.16-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./python3-sphinx-argparse_0.5.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./libmuparser2v5_2.3.4-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./rdfind_1.6.0-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./libclang1-21_21.1.8-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./libcommons-logging-java_1.3.0-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./texlive-pictures_2025.20260124-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:53] "GET /./texlive-latex-extra_2025.20260124-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:54] "GET /./mpi-default-bin_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:54] "GET /./symlinks_1.4-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:54] "GET /./libmuparser-dev_2.3.4-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:54] "GET /./python3-sphinxcontrib.autoprogram_0.1.9-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:54] "GET /./python3-networkx_3.4.2-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:54] "GET /./lsb-release_12.1-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:54] "GET /./libclang-cpp21_21.1.8-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:55] "GET /./python3-dev_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:55] "GET /./python3-mpi4py_4.1.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:55] "GET /./doxygen_1.15.0%2bds1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [14/Mar/2026 05:50:55] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmppcd1kks8/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q Reading package lists... Building dependency tree... Reading state information... libgomp1 is already the newest version (16-20260308-1). libgomp1 set to manually installed. liblz4-1 is already the newest version (1.10.0-8). liblz4-1 set to manually installed. libcap-ng0 is already the newest version (0.9.1-1). libperl5.40 is already the newest version (5.40.1-7). libperl5.40 set to manually installed. adduser is already the newest version (3.154). adduser set to manually installed. libpaper2 is already the newest version (2.2.5-0.3+b3). libpaper2 set to manually installed. readline-common is already the newest version (8.3-4). readline-common set to manually installed. dpkg is already the newest version (1.23.7). libde265-0 is already the newest version (1.0.16-1+b1). libde265-0 set to manually installed. python3-sphinx-copybutton is already the newest version (0.5.2-3). python3-sphinx-copybutton set to manually installed. libdrm2 is already the newest version (2.4.131-1). libdrm2 set to manually installed. python3-chardet is already the newest version (5.2.0+dfsg-2). python3-chardet set to manually installed. liblerc4 is already the newest version (4.0.0+ds-5+b1). liblerc4 set to manually installed. python3-numpy-dev is already the newest version (1:2.3.5+ds-3). python3-numpy-dev set to manually installed. libnuma-dev is already the newest version (2.0.19-1+b1). libnuma-dev set to manually installed. libpython3-stdlib is already the newest version (3.13.9-3). libpython3-stdlib set to manually installed. libstdc++6 is already the newest version (16-20260308-1). libstdc++6 set to manually installed. python3-accessible-pygments is already the newest version (0.0.5-2). python3-accessible-pygments set to manually installed. ghostscript is already the newest version (10.06.0~dfsg-3). ghostscript set to manually installed. procps is already the newest version (2:4.0.4-9+b1). procps set to manually installed. libbsd0 is already the newest version (0.12.2-2+b1). libbsd0 set to manually installed. libhwy1t64 is already the newest version (1.3.0-2). libhwy1t64 set to manually installed. libmpfi0 is already the newest version (1.5.4+ds-4+b1). libmpfi0 set to manually installed. python3-sphinx is already the newest version (8.2.3-12). python3-sphinx set to manually installed. graphviz is already the newest version (14.1.2-1). graphviz set to manually installed. libxml2-16 is already the newest version (2.15.1+dfsg-2+b1). libxml2-16 set to manually installed. libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. python3-pytest is already the newest version (9.0.2-4). python3-pytest set to manually installed. python3-numpy is already the newest version (1:2.3.5+ds-3). python3-numpy set to manually installed. libgvplugin-gd8 is already the newest version (14.1.2-1). libgvplugin-gd8 set to manually installed. librhash1 is already the newest version (1.4.6-1.1). librhash1 set to manually installed. libuuid1 is already the newest version (2.41.3-4). mawk is already the newest version (1.3.4.20260302-1). libevent-extra-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-extra-2.1-7t64 set to manually installed. libboost1.90-dev is already the newest version (1.90.0-5+b1). libboost1.90-dev set to manually installed. libcdt6 is already the newest version (14.1.2-1). libcdt6 set to manually installed. gfortran-15 is already the newest version (15.2.0-15). gfortran-15 set to manually installed. libhwasan0 is already the newest version (16-20260308-1). libhwasan0 set to manually installed. libdebconfclient0 is already the newest version (0.282+b2). gcc is already the newest version (4:15.2.0-5). gcc set to manually installed. cpp is already the newest version (4:15.2.0-5). cpp set to manually installed. dh-python is already the newest version (7.20260125). dh-python set to manually installed. sed is already the newest version (4.9-2). libopenjp2-7 is already the newest version (2.5.4-1). libopenjp2-7 set to manually installed. furo is already the newest version (2025.12.19+dfsg-1). furo set to manually installed. libngtcp2-16 is already the newest version (1.21.0-1). libngtcp2-16 set to manually installed. libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. libfftw3-dev is already the newest version (3.3.10-2+b2). libfftw3-dev set to manually installed. graphicsmagick is already the newest version (1.4+really1.3.46-2). graphicsmagick set to manually installed. python3-charset-normalizer is already the newest version (3.4.4-2). python3-charset-normalizer set to manually installed. libllvm21 is already the newest version (1:21.1.8-5). libllvm21 set to manually installed. libbinutils is already the newest version (2.46-3). libbinutils set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2). libxdmcp6 set to manually installed. mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. libctf0 is already the newest version (2.46-3). libctf0 set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. libavahi-common3 is already the newest version (0.8-18). libavahi-common3 set to manually installed. tar is already the newest version (1.35+dfsg-4). libc-gconv-modules-extra is already the newest version (2.42-13). libfido2-1 is already the newest version (1.16.0-2+b1). libfido2-1 set to manually installed. libidn12 is already the newest version (1.43-2+b1). libidn12 set to manually installed. mscgen is already the newest version (0.20-16). mscgen set to manually installed. docutils-common is already the newest version (0.22.4+dfsg-1). docutils-common set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. libheif1 is already the newest version (1.21.2-3). libheif1 set to manually installed. python-babel-localedata is already the newest version (2.17.0-2). python-babel-localedata set to manually installed. libfontconfig1 is already the newest version (2.17.1-5). libfontconfig1 set to manually installed. debconf is already the newest version (1.5.92). libcairo2 is already the newest version (1.18.4-3). libcairo2 set to manually installed. libsframe3 is already the newest version (2.46-3). libsframe3 set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-5). gcc-x86-64-linux-gnu set to manually installed. libacl1 is already the newest version (2.3.2-3). libgav1-2 is already the newest version (0.20.0-2). libgav1-2 set to manually installed. libpangocairo-1.0-0 is already the newest version (1.57.0-1). libpangocairo-1.0-0 set to manually installed. libfmt10 is already the newest version (10.1.1+ds1-4+b1). libfmt10 set to manually installed. libhwloc15 is already the newest version (2.13.0-2). libhwloc15 set to manually installed. libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. openssl-provider-legacy is already the newest version (3.5.5-1). libattr1 is already the newest version (1:2.5.2-4). libjsoncpp26 is already the newest version (1.9.6-5). libjsoncpp26 set to manually installed. libjpeg62-turbo is already the newest version (1:2.1.5-4). libjpeg62-turbo set to manually installed. libkpathsea6 is already the newest version (2025.20250727.75242+ds-5+b2). libkpathsea6 set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b1). libxxhash0 set to manually installed. texlive-latex-recommended is already the newest version (2025.20260124-1). texlive-latex-recommended set to manually installed. libze1 is already the newest version (1.28.2-1). libze1 set to manually installed. tzdata is already the newest version (2026a-1). tzdata set to manually installed. python3-soupsieve is already the newest version (2.8.3-1). python3-soupsieve set to manually installed. libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. libpam0g is already the newest version (1.7.0-5+b1). libnghttp2-14 is already the newest version (1.68.0-2). libnghttp2-14 set to manually installed. libboost-dev is already the newest version (1.90.0.1). libboost-dev set to manually installed. libtsan2 is already the newest version (16-20260308-1). libtsan2 set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-3). libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 set to manually installed. libnettle8t64 is already the newest version (3.10.2-1). libnettle8t64 set to manually installed. poppler-data is already the newest version (0.4.12-1). poppler-data set to manually installed. libgd3 is already the newest version (2.3.3-13+b1). libgd3 set to manually installed. libssh2-1t64 is already the newest version (1.11.1-1+b1). libssh2-1t64 set to manually installed. g++-15-x86-64-linux-gnu is already the newest version (15.2.0-15). g++-15-x86-64-linux-gnu set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. libthai-data is already the newest version (0.1.30-1). libthai-data set to manually installed. libffi8 is already the newest version (3.5.2-3+b1). libffi8 set to manually installed. t1utils is already the newest version (1.41-4). t1utils set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b1). libgdbm-compat4t64 set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-10). libsasl2-2 set to manually installed. libproc2-0 is already the newest version (2:4.0.4-9+b1). libproc2-0 set to manually installed. libsepol2 is already the newest version (3.9-2). libsepol2 set to manually installed. libsystemd0 is already the newest version (260~rc2-1). libptexenc1 is already the newest version (2025.20250727.75242+ds-5+b2). libptexenc1 set to manually installed. cmake-data is already the newest version (4.2.3-2). cmake-data set to manually installed. libibverbs-dev is already the newest version (61.0-2). libibverbs-dev set to manually installed. python3-urllib3 is already the newest version (2.6.3-1). python3-urllib3 set to manually installed. libgraphicsmagick-q16-3t64 is already the newest version (1.4+really1.3.46-2). libgraphicsmagick-q16-3t64 set to manually installed. coreutils is already the newest version (9.10-1). libkrb5support0 is already the newest version (1.22.1-2). libkrb5support0 set to manually installed. libselinux1 is already the newest version (3.9-4+b1). libgprofng0 is already the newest version (2.46-3). libgprofng0 set to manually installed. libgcc-15-dev is already the newest version (15.2.0-15). libgcc-15-dev set to manually installed. libpython3.13-dev is already the newest version (3.13.12-1). libpython3.13-dev set to manually installed. libxcb-shm0 is already the newest version (1.17.0-2+b2). libxcb-shm0 set to manually installed. libucc1 is already the newest version (1.7.0~rc1-1). libucc1 set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. python3.13-dev is already the newest version (3.13.12-1). python3.13-dev set to manually installed. libspdlog1.15 is already the newest version (1:1.15.3+ds-1+b1). libspdlog1.15 set to manually installed. libsm6 is already the newest version (2:1.2.6-1+b1). libsm6 set to manually installed. libapache-pom-java is already the newest version (33-2). libapache-pom-java set to manually installed. liblapack3 is already the newest version (3.12.1-7+b1). liblapack3 set to manually installed. python3-sphinx-inline-tabs is already the newest version (2023.4.21-3). python3-sphinx-inline-tabs set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. libfreetype6 is already the newest version (2.14.2+dfsg-1). libfreetype6 set to manually installed. libtool is already the newest version (2.5.4-9). libtool set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:15.2.0-5). cpp-x86-64-linux-gnu set to manually installed. libjbig0 is already the newest version (2.1-6.1+b3). libjbig0 set to manually installed. texlive-fonts-recommended is already the newest version (2025.20260124-1). texlive-fonts-recommended set to manually installed. python3-certifi is already the newest version (2026.2.25+ds-1). python3-certifi set to manually installed. libgs10-common is already the newest version (10.06.0~dfsg-3). libgs10-common set to manually installed. ncurses-base is already the newest version (6.6+20251231-1). xml-core is already the newest version (0.19). xml-core set to manually installed. libsemanage2 is already the newest version (3.9-1+b1). libsemanage2 set to manually installed. librdmacm1t64 is already the newest version (61.0-2). librdmacm1t64 set to manually installed. gcc-15 is already the newest version (15.2.0-15). gcc-15 set to manually installed. findutils is already the newest version (4.10.0-3). gcc-16-base is already the newest version (16-20260308-1). libaudit-common is already the newest version (1:4.1.2-1). libwebpmux3 is already the newest version (1.5.0-0.1+b1). libwebpmux3 set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. libltdl7 is already the newest version (2.5.4-9). libltdl7 set to manually installed. x11-common is already the newest version (1:7.7+26). x11-common set to manually installed. libice6 is already the newest version (2:1.1.1-1+b1). libice6 set to manually installed. libcommons-parent-java is already the newest version (56-1). libcommons-parent-java set to manually installed. libevent-dev is already the newest version (2.1.12-stable-10+b2). libevent-dev set to manually installed. base-files is already the newest version (14). libcc1-0 is already the newest version (16-20260308-1). libcc1-0 set to manually installed. dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. mount is already the newest version (2.41.3-4). mount set to manually installed. libavahi-client3 is already the newest version (0.8-18). libavahi-client3 set to manually installed. libmagic-mgc is already the newest version (1:5.46-5+b1). libmagic-mgc set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-3). zlib1g-dev set to manually installed. libmagic1t64 is already the newest version (1:5.46-5+b1). libmagic1t64 set to manually installed. fonts-lmodern is already the newest version (2.005-1). fonts-lmodern set to manually installed. sysvinit-utils is already the newest version (3.15-6). libpam-modules is already the newest version (1.7.0-5+b1). init-system-helpers is already the newest version (1.69). libxapian30 is already the newest version (1.4.31-2). libxapian30 set to manually installed. libxaw7 is already the newest version (2:1.0.16-1+b1). libxaw7 set to manually installed. libsvtav1enc2 is already the newest version (2.3.0+dfsg-1). libsvtav1enc2 set to manually installed. python3-jinja2 is already the newest version (3.1.6-1). python3-jinja2 set to manually installed. libgfortran-15-dev is already the newest version (15.2.0-15). libgfortran-15-dev set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1). libfabric1 is already the newest version (2.1.0-1.1+b1). libfabric1 set to manually installed. libpciaccess0 is already the newest version (0.17-3+b4). libpciaccess0 set to manually installed. cpp-15 is already the newest version (15.2.0-15). cpp-15 set to manually installed. libyuv0 is already the newest version (0.0.1922.20260106-1). libyuv0 set to manually installed. preview-latex-style is already the newest version (13.2-1.1). preview-latex-style set to manually installed. libpixman-1-0 is already the newest version (0.46.4-1+b1). libpixman-1-0 set to manually installed. python3-pygments is already the newest version (2.19.2+dfsg-1). python3-pygments set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11). libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libnl-route-3-200 is already the newest version (3.12.0-2). libnl-route-3-200 set to manually installed. python3-pybind11 is already the newest version (3.0.1-3). python3-pybind11 set to manually installed. liblsan0 is already the newest version (16-20260308-1). liblsan0 set to manually installed. libzzip-0-13t64 is already the newest version (0.13.78+dfsg.1-0.2). libzzip-0-13t64 set to manually installed. libcups2t64 is already the newest version (2.4.16-1). libcups2t64 set to manually installed. libimagequant0 is already the newest version (4.4.1-1+b1). libimagequant0 set to manually installed. libcurl4t64 is already the newest version (8.19.0~rc3-1). libcurl4t64 set to manually installed. tex-gyre is already the newest version (20180621-7). tex-gyre set to manually installed. libatomic1 is already the newest version (16-20260308-1). libatomic1 set to manually installed. libgssapi-krb5-2 is already the newest version (1.22.1-2). libgssapi-krb5-2 set to manually installed. liblapack-dev is already the newest version (3.12.1-7+b1). liblapack-dev set to manually installed. xfonts-utils is already the newest version (1:7.7+7). xfonts-utils set to manually installed. libkrb5-3 is already the newest version (1.22.1-2). libkrb5-3 set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-15). cpp-15-x86-64-linux-gnu set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. libpsl5t64 is already the newest version (0.21.2-1.1+b2). libpsl5t64 set to manually installed. libxi6 is already the newest version (2:1.8.2-2). libxi6 set to manually installed. libprrte-dev is already the newest version (3.0.13-2). libprrte-dev set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. libcgraph8 is already the newest version (14.1.2-1). libcgraph8 set to manually installed. libtiff6 is already the newest version (4.7.1-1). libtiff6 set to manually installed. python3-requests is already the newest version (2.32.5+dfsg-1). python3-requests set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. libnuma1 is already the newest version (2.0.19-1+b1). libnuma1 set to manually installed. texlive-base is already the newest version (2025.20260124-1). texlive-base set to manually installed. libarchive13t64 is already the newest version (3.8.5-1). libarchive13t64 set to manually installed. texlive-binaries is already the newest version (2025.20250727.75242+ds-5+b2). texlive-binaries set to manually installed. libuv1t64 is already the newest version (1.51.0-2+b1). libuv1t64 set to manually installed. python3-markupsafe is already the newest version (3.0.3-1+b1). python3-markupsafe set to manually installed. libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. perl is already the newest version (5.40.1-7). perl set to manually installed. gcc-15-base is already the newest version (15.2.0-15). gcc-15-base set to manually installed. libxt6t64 is already the newest version (1:1.2.1-1.3+b1). libxt6t64 set to manually installed. libpdfbox-java is already the newest version (1:1.8.16-5). libpdfbox-java set to manually installed. xz-utils is already the newest version (5.8.2-2). xz-utils set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.4-1). ocl-icd-libopencl1 set to manually installed. libtexlua53-5 is already the newest version (2025.20250727.75242+ds-5+b2). libtexlua53-5 set to manually installed. libevent-core-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-core-2.1-7t64 set to manually installed. libdav1d7 is already the newest version (1.5.3-1+b1). libdav1d7 set to manually installed. bzip2 is already the newest version (1.0.8-6+b1). bzip2 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-15). gcc-15-x86-64-linux-gnu set to manually installed. python3-sphinx-argparse is already the newest version (0.5.2-1). python3-sphinx-argparse set to manually installed. autopoint is already the newest version (0.23.2-1). autopoint set to manually installed. ca-certificates is already the newest version (20260223). ca-certificates set to manually installed. libthai0 is already the newest version (0.1.30-1). libthai0 set to manually installed. tex-common is already the newest version (6.20). tex-common set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-10). libsasl2-modules-db set to manually installed. python3 is already the newest version (3.13.9-3). python3 set to manually installed. dash is already the newest version (0.5.12-12). libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. libijs-0.35 is already the newest version (0.35-16+b1). libijs-0.35 set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. libxdot4 is already the newest version (14.1.2-1). libxdot4 set to manually installed. libncursesw6 is already the newest version (6.6+20251231-1). libncursesw6 set to manually installed. libmuparser2v5 is already the newest version (2.3.4-2). libmuparser2v5 set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b1). libkeyutils1 set to manually installed. file is already the newest version (1:5.46-5+b1). file set to manually installed. libltdl-dev is already the newest version (2.5.4-9). libltdl-dev set to manually installed. libprrte3 is already the newest version (3.0.13-2). libprrte3 set to manually installed. libabsl20240722 is already the newest version (20240722.0-4). libabsl20240722 set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.46-3). binutils-x86-64-linux-gnu set to manually installed. rdfind is already the newest version (1.6.0-1+b1). rdfind set to manually installed. libclang1-21 is already the newest version (1:21.1.8-5). libclang1-21 set to manually installed. libglib2.0-0t64 is already the newest version (2.87.2-3). libglib2.0-0t64 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libnl-3-dev is already the newest version (3.12.0-2). libnl-3-dev set to manually installed. xdg-utils is already the newest version (1.2.1-2). xdg-utils set to manually installed. python3.13 is already the newest version (3.13.12-1). python3.13 set to manually installed. python3-pluggy is already the newest version (1.6.0-2). python3-pluggy set to manually installed. texlive-latex-extra is already the newest version (2025.20260124-1). texlive-latex-extra set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b1). libuchardet0 set to manually installed. libquadmath0 is already the newest version (16-20260308-1). libquadmath0 set to manually installed. libpython3.13-minimal is already the newest version (3.13.12-1). libpython3.13-minimal set to manually installed. mpi-default-bin is already the newest version (1.20). mpi-default-bin set to manually installed. symlinks is already the newest version (1.4-5+b1). symlinks set to manually installed. libpng16-16t64 is already the newest version (1.6.55-1). libpng16-16t64 set to manually installed. diffutils is already the newest version (1:3.12-1). libfontenc1 is already the newest version (1:1.1.8-1+b3). libfontenc1 set to manually installed. sphinx-common is already the newest version (8.2.3-12). sphinx-common set to manually installed. libgraphite2-3 is already the newest version (1.3.14-11+b1). libgraphite2-3 set to manually installed. libudev1 is already the newest version (260~rc2-1). libpython3-dev is already the newest version (3.13.9-3). libpython3-dev set to manually installed. python3-bs4 is already the newest version (4.14.3-2). python3-bs4 set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. libelf1t64 is already the newest version (0.194-1). libelf1t64 set to manually installed. liblzma5 is already the newest version (5.8.2-2). dwz is already the newest version (0.16-2). dwz set to manually installed. libclang-common-21-dev is already the newest version (1:21.1.8-5). libclang-common-21-dev set to manually installed. libavif16 is already the newest version (1.3.0-1+b2). libavif16 set to manually installed. libpaper-utils is already the newest version (2.2.5-0.3+b3). libpaper-utils set to manually installed. libsystemd-shared is already the newest version (260~rc2-1). libsystemd-shared set to manually installed. gzip is already the newest version (1.13-1). libdeflate0 is already the newest version (1.23-2+b1). libdeflate0 set to manually installed. bash is already the newest version (5.3-2). libfftw3-single3 is already the newest version (3.3.10-2+b2). libfftw3-single3 set to manually installed. libasan8 is already the newest version (16-20260308-1). libasan8 set to manually installed. openssh-client is already the newest version (1:10.2p1-5). openssh-client set to manually installed. util-linux is already the newest version (2.41.3-4). dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. debhelper is already the newest version (13.31). debhelper set to manually installed. libgs10 is already the newest version (10.06.0~dfsg-3). libgs10 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.21.0-1). libngtcp2-crypto-ossl0 set to manually installed. libpotrace0 is already the newest version (1.16-2+b3). libpotrace0 set to manually installed. openssl is already the newest version (3.5.5-1). openssl set to manually installed. libfftw3-quad3 is already the newest version (3.3.10-2+b2). libfftw3-quad3 set to manually installed. libgnutls30t64 is already the newest version (3.8.12-3). libgnutls30t64 set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b1). binutils is already the newest version (2.46-3). binutils set to manually installed. grep is already the newest version (3.12-1). libwmflite-0.2-7 is already the newest version (0.2.14-1). libwmflite-0.2-7 set to manually installed. libgs-common is already the newest version (10.06.0~dfsg-3). libgs-common set to manually installed. libxpm4 is already the newest version (1:3.5.17-1+b4). libxpm4 set to manually installed. libcbor0.10 is already the newest version (0.10.2-2.1). libcbor0.10 set to manually installed. libtext-wrapi18n-perl is already the newest version (0.06-10). libtext-wrapi18n-perl set to manually installed. libibmad5 is already the newest version (61.0-2). libibmad5 set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-15). libstdc++-15-dev set to manually installed. python3-iniconfig is already the newest version (2.1.0-2). python3-iniconfig set to manually installed. libmunge2 is already the newest version (0.5.16-1.1). libmunge2 set to manually installed. libpathplan4 is already the newest version (14.1.2-1). libpathplan4 set to manually installed. libfontbox-java is already the newest version (1:1.8.16-5). libfontbox-java set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-pthreads-2.1-7t64 set to manually installed. pybind11-dev is already the newest version (3.0.1-3). pybind11-dev set to manually installed. libsqlite3-0 is already the newest version (3.46.1-9+b1). libsqlite3-0 set to manually installed. fontconfig-config is already the newest version (2.17.1-5). fontconfig-config set to manually installed. libpython3.13 is already the newest version (3.13.12-1). libpython3.13 set to manually installed. python3-roman-numerals is already the newest version (4.1.0-1). python3-roman-numerals set to manually installed. fonts-urw-base35 is already the newest version (20200910-8). fonts-urw-base35 set to manually installed. libgcc-s1 is already the newest version (16-20260308-1). libmuparser-dev is already the newest version (2.3.4-2). libmuparser-dev set to manually installed. libgfortran5 is already the newest version (16-20260308-1). libgfortran5 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b1). bash-completion is already the newest version (1:2.16.0-8). bash-completion set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libsynctex2 is already the newest version (2025.20250727.75242+ds-5+b2). libsynctex2 set to manually installed. libavahi-common-data is already the newest version (0.8-18). libavahi-common-data set to manually installed. libucx0 is already the newest version (1.20.0+ds-4). libucx0 set to manually installed. libsemanage-common is already the newest version (3.9-1). libsemanage-common set to manually installed. libblas3 is already the newest version (3.12.1-7+b1). libblas3 set to manually installed. libgvplugin-pango8 is already the newest version (14.1.2-1). libgvplugin-pango8 set to manually installed. libxrender1 is already the newest version (1:0.9.12-1+b1). libxrender1 set to manually installed. libpango-1.0-0 is already the newest version (1.57.0-1). libpango-1.0-0 set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. python3-docutils is already the newest version (0.22.4+dfsg-1). python3-docutils set to manually installed. libsharpyuv0 is already the newest version (1.5.0-0.1+b1). libsharpyuv0 set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libpangoft2-1.0-0 is already the newest version (1.57.0-1). libpangoft2-1.0-0 set to manually installed. libtext-charwidth-perl is already the newest version (0.04-11+b5). libtext-charwidth-perl set to manually installed. libevent-openssl-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-openssl-2.1-7t64 set to manually installed. python3-minimal is already the newest version (3.13.9-3). python3-minimal set to manually installed. gettext is already the newest version (0.23.2-1). gettext set to manually installed. autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. libk5crypto3 is already the newest version (1.22.1-2). libk5crypto3 set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1). libfftw3-bin is already the newest version (3.3.10-2+b2). libfftw3-bin set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. libreadline8t64 is already the newest version (8.3-4). libreadline8t64 set to manually installed. gfortran-15-x86-64-linux-gnu is already the newest version (15.2.0-15). gfortran-15-x86-64-linux-gnu set to manually installed. python3-sphinxcontrib.autoprogram is already the newest version (0.1.9-1). python3-sphinxcontrib.autoprogram set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b1). linux-libc-dev is already the newest version (6.19.6-1). linux-libc-dev set to manually installed. libgvc7 is already the newest version (14.1.2-1). libgvc7 set to manually installed. hostname is already the newest version (3.25). libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:15.2.0-5). g++-x86-64-linux-gnu set to manually installed. libmount1 is already the newest version (2.41.3-4). libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. g++-15 is already the newest version (15.2.0-15). g++-15 set to manually installed. base-passwd is already the newest version (3.6.8). libssl3t64 is already the newest version (3.5.5-1). libprrte-bin is already the newest version (3.0.13-2). libprrte-bin set to manually installed. perl-base is already the newest version (5.40.1-7). libctf-nobfd0 is already the newest version (2.46-3). libctf-nobfd0 set to manually installed. python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. python3.13-minimal is already the newest version (3.13.12-1). python3.13-minimal set to manually installed. libfftw3-long3 is already the newest version (3.3.10-2+b2). libfftw3-long3 set to manually installed. libblas-dev is already the newest version (3.12.1-7+b1). libblas-dev set to manually installed. libmpc3 is already the newest version (1.3.1-2+b1). libmpc3 set to manually installed. libpython3.13-stdlib is already the newest version (3.13.12-1). libpython3.13-stdlib set to manually installed. libubsan1 is already the newest version (16-20260308-1). libubsan1 set to manually installed. libc6-dev is already the newest version (2.42-13). libc6-dev set to manually installed. libfftw3-double3 is already the newest version (3.3.10-2+b2). libfftw3-double3 set to manually installed. libc6 is already the newest version (2.42-13). libibumad3 is already the newest version (61.0-2). libibumad3 set to manually installed. librav1e0.8 is already the newest version (0.8.1-7). librav1e0.8 set to manually installed. libdatrie1 is already the newest version (0.2.14-1). libdatrie1 set to manually installed. libc-bin is already the newest version (2.42-13). passwd is already the newest version (1:4.19.3-1). passwd set to manually installed. libz3-4 is already the newest version (4.13.3-1+b1). libz3-4 set to manually installed. python3-alabaster is already the newest version (1.0.0-1). python3-alabaster set to manually installed. architecture-properties is already the newest version (0.2.6+b1). architecture-properties set to manually installed. autoconf is already the newest version (2.72-6). autoconf set to manually installed. libtasn1-6 is already the newest version (4.21.0-2). libtasn1-6 set to manually installed. libexpat1 is already the newest version (2.7.4-1). libexpat1 set to manually installed. cmake is already the newest version (4.2.3-2). cmake set to manually installed. liblcms2-2 is already the newest version (2.17-1). liblcms2-2 set to manually installed. libnl-route-3-dev is already the newest version (3.12.0-2). libnl-route-3-dev set to manually installed. python3-idna is already the newest version (3.11-1). python3-idna set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-2.1-7t64 set to manually installed. libharfbuzz0b is already the newest version (12.3.2-2+b2). libharfbuzz0b set to manually installed. python3-typing-extensions is already the newest version (4.15.0-2). python3-typing-extensions set to manually installed. login.defs is already the newest version (1:4.19.3-1). login.defs set to manually installed. xfonts-encodings is already the newest version (1:1.0.4-2.2). xfonts-encodings set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1). libpipeline1 is already the newest version (1.5.8-2). libpipeline1 set to manually installed. libitm1 is already the newest version (16-20260308-1). libitm1 set to manually installed. libjs-sphinxdoc is already the newest version (8.2.3-12). libjs-sphinxdoc set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b1). libxau6 set to manually installed. libcommons-logging-java is already the newest version (1.3.0-2). libcommons-logging-java set to manually installed. libdebhelper-perl is already the newest version (13.31). libdebhelper-perl set to manually installed. libhwloc-plugins is already the newest version (2.13.0-2). libhwloc-plugins set to manually installed. libnl-3-200 is already the newest version (3.12.0-2). libnl-3-200 set to manually installed. libfribidi0 is already the newest version (1.0.16-5). libfribidi0 set to manually installed. automake is already the newest version (1:1.18.1-4). automake set to manually installed. libgvpr2 is already the newest version (14.1.2-1). libgvpr2 set to manually installed. python3-packaging is already the newest version (25.0-2). python3-packaging set to manually installed. libteckit0 is already the newest version (2.5.13+ds-1). libteckit0 set to manually installed. libdbus-1-3 is already the newest version (1.16.2-4). libdbus-1-3 set to manually installed. libidn2-0 is already the newest version (2.3.8-4+b1). libidn2-0 set to manually installed. python3-defusedxml is already the newest version (0.7.1-3). python3-defusedxml set to manually installed. bsdextrautils is already the newest version (2.41.3-4). bsdextrautils set to manually installed. libpam-runtime is already the newest version (1.7.0-5). python3-networkx is already the newest version (3.4.2-4). python3-networkx set to manually installed. texlive-latex-base is already the newest version (2025.20260124-1). texlive-latex-base set to manually installed. libgdbm6t64 is already the newest version (1.26-1+b1). libgdbm6t64 set to manually installed. libsmartcols1 is already the newest version (2.41.3-4). libjs-jquery is already the newest version (3.7.1+dfsg+~3.5.33-1). libjs-jquery set to manually installed. libwebp7 is already the newest version (1.5.0-0.1+b1). libwebp7 set to manually installed. libdrm-amdgpu1 is already the newest version (2.4.131-1). libdrm-amdgpu1 set to manually installed. sphinx-basic-ng is already the newest version (1.0.0~beta2-1). sphinx-basic-ng set to manually installed. libheif-plugin-dav1d is already the newest version (1.21.2-3). libheif-plugin-dav1d set to manually installed. texlive-pictures is already the newest version (2025.20260124-1). texlive-pictures set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5+b1). libaom3 is already the newest version (3.13.1-2). libaom3 set to manually installed. libp11-kit0 is already the newest version (0.26.2-2). libp11-kit0 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1+b1). libldap2 set to manually installed. libblkid1 is already the newest version (2.41.3-4). sgml-base is already the newest version (1.31+nmu1). sgml-base set to manually installed. libedit2 is already the newest version (3.1-20251016-1). libedit2 set to manually installed. libjson-perl is already the newest version (4.10000-1). libjson-perl set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b1). pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. libisl23 is already the newest version (0.27-1+b1). libisl23 set to manually installed. lsb-release is already the newest version (12.1-2). lsb-release set to manually installed. media-types is already the newest version (14.0.0). media-types set to manually installed. libexpat1-dev is already the newest version (2.7.4-1). libexpat1-dev set to manually installed. fontconfig is already the newest version (2.17.1-5). fontconfig set to manually installed. gettext-base is already the newest version (0.23.2-1). gettext-base set to manually installed. libxmu6 is already the newest version (2:1.1.3-4). libxmu6 set to manually installed. ibverbs-providers is already the newest version (61.0-2). ibverbs-providers set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-3+b1). librtmp1 set to manually installed. libclang-cpp21 is already the newest version (1:21.1.8-5). libclang-cpp21 set to manually installed. python3-snowballstemmer is already the newest version (3.0.1-1). python3-snowballstemmer set to manually installed. systemd is already the newest version (260~rc2-1). systemd set to manually installed. libibverbs1 is already the newest version (61.0-2). libibverbs1 set to manually installed. libhogweed6t64 is already the newest version (3.10.2-1). libhogweed6t64 set to manually installed. libjbig2dec0 is already the newest version (0.20-1+b4). libjbig2dec0 set to manually installed. python3-dev is already the newest version (3.13.9-3). python3-dev set to manually installed. libfuse3-4 is already the newest version (3.18.1-1). libfuse3-4 set to manually installed. libdrm-common is already the newest version (2.4.131-1). libdrm-common set to manually installed. libicu78 is already the newest version (78.2-2). libicu78 set to manually installed. libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. python3-mpi4py is already the newest version (4.1.1-1+b1). python3-mpi4py set to manually installed. libheif-plugin-libde265 is already the newest version (1.21.2-3). libheif-plugin-libde265 set to manually installed. libc-dev-bin is already the newest version (2.42-13). libc-dev-bin set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. debianutils is already the newest version (5.23.2). libmd0 is already the newest version (1.1.0-2+b2). libxcb-render0 is already the newest version (1.17.0-2+b2). libxcb-render0 set to manually installed. binutils-common is already the newest version (2.46-3). binutils-common set to manually installed. libmpfr6 is already the newest version (4.2.2-2+b1). libmpfr6 set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. libhwloc-dev is already the newest version (2.13.0-2). libhwloc-dev set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. doxygen is already the newest version (1.15.0+ds1-1+b1). doxygen set to manually installed. libjxl0.11 is already the newest version (0.11.1-6). libjxl0.11 set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. python3-babel is already the newest version (2.17.0-2). python3-babel set to manually installed. ucf is already the newest version (3.0052). ucf set to manually installed. g++ is already the newest version (4:15.2.0-5). g++ set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3). libpmix2t64 set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q (Reading database ... 78362 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.vObhvHzu8q... I: success in 207.2019 seconds Downloading dependency 383 of 466: libharfbuzz0b:amd64=12.3.2-2+b2 Downloading dependency 384 of 466: python3-typing-extensions:amd64=4.15.0-2 Downloading dependency 385 of 466: login.defs:amd64=1:4.19.3-1 Downloading dependency 386 of 466: xfonts-encodings:amd64=1:1.0.4-2.2 Downloading dependency 387 of 466: ncurses-bin:amd64=6.6+20251231-1 Downloading dependency 388 of 466: libpipeline1:amd64=1.5.8-2 Downloading dependency 389 of 466: libitm1:amd64=16-20260308-1 Downloading dependency 390 of 466: libjs-sphinxdoc:amd64=8.2.3-12 Downloading dependency 391 of 466: libxau6:amd64=1:1.0.11-1+b1 Downloading dependency 392 of 466: libcommons-logging-java:amd64=1.3.0-2 Downloading dependency 393 of 466: libdebhelper-perl:amd64=13.31 Downloading dependency 394 of 466: libhwloc-plugins:amd64=2.13.0-2 Downloading dependency 395 of 466: libnl-3-200:amd64=3.12.0-2 Downloading dependency 396 of 466: libfribidi0:amd64=1.0.16-5 Downloading dependency 397 of 466: automake:amd64=1:1.18.1-4 Downloading dependency 398 of 466: libgvpr2:amd64=14.1.2-1 Downloading dependency 399 of 466: python3-packaging:amd64=25.0-2 Downloading dependency 400 of 466: libteckit0:amd64=2.5.13+ds-1 Downloading dependency 401 of 466: libdbus-1-3:amd64=1.16.2-4 Downloading dependency 402 of 466: libidn2-0:amd64=2.3.8-4+b1 Downloading dependency 403 of 466: python3-defusedxml:amd64=0.7.1-3 Downloading dependency 404 of 466: bsdextrautils:amd64=2.41.3-4 Downloading dependency 405 of 466: libpam-runtime:amd64=1.7.0-5 Downloading dependency 406 of 466: python3-networkx:amd64=3.4.2-4 Downloading dependency 407 of 466: texlive-latex-base:amd64=2025.20260124-1 Downloading dependency 408 of 466: libgdbm6t64:amd64=1.26-1+b1 Downloading dependency 409 of 466: libsmartcols1:amd64=2.41.3-4 Downloading dependency 410 of 466: libjs-jquery:amd64=3.7.1+dfsg+~3.5.33-1 Downloading dependency 411 of 466: libwebp7:amd64=1.5.0-0.1+b1 Downloading dependency 412 of 466: libdrm-amdgpu1:amd64=2.4.131-1 Downloading dependency 413 of 466: sphinx-basic-ng:amd64=1.0.0~beta2-1 Downloading dependency 414 of 466: libheif-plugin-dav1d:amd64=1.21.2-3 Downloading dependency 415 of 466: texlive-pictures:amd64=2025.20260124-1 Downloading dependency 416 of 466: libpam-modules-bin:amd64=1.7.0-5+b1 Downloading dependency 417 of 466: libaom3:amd64=3.13.1-2 Downloading dependency 418 of 466: libp11-kit0:amd64=0.26.2-2 Downloading dependency 419 of 466: libxnvctrl0:amd64=535.171.04-1+b3 Downloading dependency 420 of 466: make:amd64=4.4.1-3 Downloading dependency 421 of 466: libldap2:amd64=2.6.10+dfsg-1+b1 Downloading dependency 422 of 466: libblkid1:amd64=2.41.3-4 Downloading dependency 423 of 466: sgml-base:amd64=1.31+nmu1 Downloading dependency 424 of 466: libedit2:amd64=3.1-20251016-1 Downloading dependency 425 of 466: libjson-perl:amd64=4.10000-1 Downloading dependency 426 of 466: libpcre2-8-0:amd64=10.46-1+b1 Downloading dependency 427 of 466: pkgconf-bin:amd64=2.5.1-4 Downloading dependency 428 of 466: libisl23:amd64=0.27-1+b1 Downloading dependency 429 of 466: lsb-release:amd64=12.1-2 Downloading dependency 430 of 466: media-types:amd64=14.0.0 Downloading dependency 431 of 466: libexpat1-dev:amd64=2.7.4-1 Downloading dependency 432 of 466: fontconfig:amd64=2.17.1-5 Downloading dependency 433 of 466: gettext-base:amd64=0.23.2-1 Downloading dependency 434 of 466: libxmu6:amd64=2:1.1.3-4 Downloading dependency 435 of 466: ibverbs-providers:amd64=61.0-2 Downloading dependency 436 of 466: librtmp1:amd64=2.4+20151223.gitfa8646d.1-3+b1 Downloading dependency 437 of 466: libclang-cpp21:amd64=1:21.1.8-5 Downloading dependency 438 of 466: python3-snowballstemmer:amd64=3.0.1-1 Downloading dependency 439 of 466: systemd:amd64=260~rc2-1 Downloading dependency 440 of 466: libibverbs1:amd64=61.0-2 Downloading dependency 441 of 466: libhogweed6t64:amd64=3.10.2-1 Downloading dependency 442 of 466: libjbig2dec0:amd64=0.20-1+b4 Downloading dependency 443 of 466: python3-dev:amd64=3.13.9-3 Downloading dependency 444 of 466: libfuse3-4:amd64=3.18.1-1 Downloading dependency 445 of 466: libdrm-common:amd64=2.4.131-1 Downloading dependency 446 of 466: libicu78:amd64=78.2-2 Downloading dependency 447 of 466: libnghttp3-9:amd64=1.15.0-1 Downloading dependency 448 of 466: python3-mpi4py:amd64=4.1.1-1+b1 Downloading dependency 449 of 466: libheif-plugin-libde265:amd64=1.21.2-3 Downloading dependency 450 of 466: libc-dev-bin:amd64=2.42-13 Downloading dependency 451 of 466: po-debconf:amd64=1.0.22 Downloading dependency 452 of 466: debianutils:amd64=5.23.2 Downloading dependency 453 of 466: libmd0:amd64=1.1.0-2+b2 Downloading dependency 454 of 466: libxcb-render0:amd64=1.17.0-2+b2 Downloading dependency 455 of 466: binutils-common:amd64=2.46-3 Downloading dependency 456 of 466: libmpfr6:amd64=4.2.2-2+b1 Downloading dependency 457 of 466: libseccomp2:amd64=2.6.0-2+b1 Downloading dependency 458 of 466: libhwloc-dev:amd64=2.13.0-2 Downloading dependency 459 of 466: perl-modules-5.40:amd64=5.40.1-7 Downloading dependency 460 of 466: doxygen:amd64=1.15.0+ds1-1+b1 Downloading dependency 461 of 466: libjxl0.11:amd64=0.11.1-6 Downloading dependency 462 of 466: libopenmpi40:amd64=5.0.10-1 Downloading dependency 463 of 466: python3-babel:amd64=2.17.0-2 Downloading dependency 464 of 466: ucf:amd64=3.0052 Downloading dependency 465 of 466: g++:amd64=4:15.2.0-5 Downloading dependency 466 of 466: libpmix2t64:amd64=6.0.0+really5.0.9-3 env --chdir=/srv/rebuilderd/tmp/rebuilderdhyV6gx/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1772897449 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuild9Oa6Vg/debrebuild.sbuildrc.O6rbPo92pYdM sbuild --build=amd64 --host=amd64 --no-arch-any --arch-all --chroot=/srv/rebuilderd/tmp/debrebuild9Oa6Vg/debrebuild.tar.xKMaxkKwdmfC --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --no-source --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=gromacs-2026.1 /srv/rebuilderd/tmp/rebuilderdhyV6gx/inputs/gromacs_2026.1-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on ionos25-amd64.debian.net +==============================================================================+ | gromacs 2026.1-1 (amd64) Sat, 14 Mar 2026 05:54:06 +0000 | +==============================================================================+ Package: gromacs Version: 2026.1-1 Source Version: 2026.1-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: all I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuild9Oa6Vg/debrebuild.tar.xKMaxkKwdmfC to /srv/rebuilderd/tmp/tmp.sbuild.ljilHAupZs... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Sat, 14 Mar 2026 05:54:17 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdhyV6gx/inputs/gromacs_2026.1-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdhyV6gx/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 14 Mar 2026 05:54:20 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra Filtered Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-KDVRXQ/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Sat, 14 Mar 2026 05:54:28 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sat, 14 Mar 2026 05:54:29 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.74+deb13+1-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.74-2 (2026-03-08) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-15_15.2.0-15 gcc-15_15.2.0-15 libc6-dev_2.42-13 libstdc++-15-dev_15.2.0-15 libstdc++6_16-20260308-1 linux-libc-dev_6.19.6-1 Package versions: adduser_3.154 architecture-properties_0.2.6+b1 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-2 bash-completion_1:2.16.0-8 binutils_2.46-3 binutils-common_2.46-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.41.3-4 build-essential_12.12 bzip2_1.0.8-6+b1 ca-certificates_20260223 cmake_4.2.3-2 cmake-data_4.2.3-2 coreutils_9.10-1 cpp_4:15.2.0-5 cpp-15_15.2.0-15 cpp-15-x86-64-linux-gnu_15.2.0-15 cpp-x86-64-linux-gnu_4:15.2.0-5 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debianutils_5.23.2 dh-autoreconf_22 dh-python_7.20260125 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 docutils-common_0.22.4+dfsg-1 doxygen_1.15.0+ds1-1+b1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-2 file_1:5.46-5+b1 findutils_4.10.0-3 fontconfig_2.17.1-5 fontconfig-config_2.17.1-5 fonts-lmodern_2.005-1 fonts-urw-base35_20200910-8 furo_2025.12.19+dfsg-1 g++_4:15.2.0-5 g++-15_15.2.0-15 g++-15-x86-64-linux-gnu_15.2.0-15 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-15_15.2.0-15 gcc-15-base_15.2.0-15 gcc-15-x86-64-linux-gnu_15.2.0-15 gcc-16-base_16-20260308-1 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-1 gettext-base_0.23.2-1 gfortran-15_15.2.0-15 gfortran-15-x86-64-linux-gnu_15.2.0-15 ghostscript_10.06.0~dfsg-3 graphicsmagick_1.4+really1.3.46-2 graphviz_14.1.2-1 grep_3.12-1 groff-base_1.23.0-10 gzip_1.13-1 hostname_3.25 ibverbs-providers_61.0-2 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libabsl20240722_20240722.0-4 libacl1_2.3.2-3 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libaom3_3.13.1-2 libapache-pom-java_33-2 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.5-1 libasan8_16-20260308-1 libatomic1_16-20260308-1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libavahi-client3_0.8-18 libavahi-common-data_0.8-18 libavahi-common3_0.8-18 libavif16_1.3.0-1+b2 libbinutils_2.46-3 libblas-dev_3.12.1-7+b1 libblas3_3.12.1-7+b1 libblkid1_2.41.3-4 libboost-dev_1.90.0.1 libboost1.90-dev_1.90.0-5+b1 libbrotli1_1.2.0-3 libbsd0_0.12.2-2+b1 libbz2-1.0_1.0.8-6+b1 libc-bin_2.42-13 libc-dev-bin_2.42-13 libc-gconv-modules-extra_2.42-13 libc6_2.42-13 libc6-dev_2.42-13 libcairo2_1.18.4-3 libcap-ng0_0.9.1-1 libcbor0.10_0.10.2-2.1 libcc1-0_16-20260308-1 libcdt6_14.1.2-1 libcgraph8_14.1.2-1 libclang-common-21-dev_1:21.1.8-5 libclang-cpp21_1:21.1.8-5 libclang1-21_1:21.1.8-5 libcom-err2_1.47.4-1 libcommons-logging-java_1.3.0-2 libcommons-parent-java_56-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcups2t64_2.4.16-1 libcurl4t64_8.19.0~rc3-1 libdatrie1_0.2.14-1 libdav1d7_1.5.3-1+b1 libdb5.3t64_5.3.28+dfsg2-11 libdbus-1-3_1.16.2-4 libde265-0_1.0.16-1+b1 libdebconfclient0_0.282+b2 libdebhelper-perl_13.31 libdeflate0_1.23-2+b1 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.131-1 libdrm-common_2.4.131-1 libdrm2_2.4.131-1 libedit2_3.1-20251016-1 libelf1t64_0.194-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libevent-core-2.1-7t64_2.1.12-stable-10+b2 libevent-dev_2.1.12-stable-10+b2 libevent-extra-2.1-7t64_2.1.12-stable-10+b2 libevent-openssl-2.1-7t64_2.1.12-stable-10+b2 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2 libexpat1_2.7.4-1 libexpat1-dev_2.7.4-1 libfabric1_2.1.0-1.1+b1 libffi8_3.5.2-3+b1 libfftw3-bin_3.3.10-2+b2 libfftw3-dev_3.3.10-2+b2 libfftw3-double3_3.3.10-2+b2 libfftw3-long3_3.3.10-2+b2 libfftw3-quad3_3.3.10-2+b2 libfftw3-single3_3.3.10-2+b2 libfido2-1_1.16.0-2+b1 libfile-stripnondeterminism-perl_1.15.0-1 libfmt10_10.1.1+ds1-4+b1 libfontbox-java_1:1.8.16-5 libfontconfig1_2.17.1-5 libfontenc1_1:1.1.8-1+b3 libfreetype6_2.14.2+dfsg-1 libfribidi0_1.0.16-5 libfuse3-4_3.18.1-1 libgav1-2_0.20.0-2 libgcc-15-dev_15.2.0-15 libgcc-s1_16-20260308-1 libgd3_2.3.3-13+b1 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgfortran-15-dev_15.2.0-15 libgfortran5_16-20260308-1 libglib2.0-0t64_2.87.2-3 libgmp10_2:6.3.0+dfsg-5+b1 libgnutls30t64_3.8.12-3 libgomp1_16-20260308-1 libgprofng0_2.46-3 libgraphicsmagick-q16-3t64_1.4+really1.3.46-2 libgraphite2-3_1.3.14-11+b1 libgs-common_10.06.0~dfsg-3 libgs10_10.06.0~dfsg-3 libgs10-common_10.06.0~dfsg-3 libgssapi-krb5-2_1.22.1-2 libgvc7_14.1.2-1 libgvplugin-gd8_14.1.2-1 libgvplugin-pango8_14.1.2-1 libgvpr2_14.1.2-1 libharfbuzz0b_12.3.2-2+b2 libheif-plugin-dav1d_1.21.2-3 libheif-plugin-libde265_1.21.2-3 libheif1_1.21.2-3 libhogweed6t64_3.10.2-1 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16-20260308-1 libhwloc-dev_2.13.0-2 libhwloc-plugins_2.13.0-2 libhwloc15_2.13.0-2 libhwy1t64_1.3.0-2 libibmad5_61.0-2 libibumad3_61.0-2 libibverbs-dev_61.0-2 libibverbs1_61.0-2 libice6_2:1.1.1-1+b1 libicu78_78.2-2 libidn12_1.43-2+b1 libidn2-0_2.3.8-4+b1 libijs-0.35_0.35-16+b1 libimagequant0_4.4.1-1+b1 libisl23_0.27-1+b1 libitm1_16-20260308-1 libjansson4_2.14-2+b4 libjbig0_2.1-6.1+b3 libjbig2dec0_0.20-1+b4 libjpeg62-turbo_1:2.1.5-4 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_8.2.3-12 libjson-perl_4.10000-1 libjsoncpp26_1.9.6-5 libjxl0.11_0.11.1-6 libk5crypto3_1.22.1-2 libkeyutils1_1.6.3-6+b1 libkpathsea6_2025.20250727.75242+ds-5+b2 libkrb5-3_1.22.1-2 libkrb5support0_1.22.1-2 liblapack-dev_3.12.1-7+b1 liblapack3_3.12.1-7+b1 liblcms2-2_2.17-1 libldap2_2.6.10+dfsg-1+b1 liblerc4_4.0.0+ds-5+b1 libllvm21_1:21.1.8-5 liblsan0_16-20260308-1 libltdl-dev_2.5.4-9 libltdl7_2.5.4-9 liblz4-1_1.10.0-8 liblzma5_5.8.2-2 libmagic-mgc_1:5.46-5+b1 libmagic1t64_1:5.46-5+b1 libmd0_1.1.0-2+b2 libmount1_2.41.3-4 libmpc3_1.3.1-2+b1 libmpfi0_1.5.4+ds-4+b1 libmpfr6_4.2.2-2+b1 libmunge2_0.5.16-1.1 libmuparser-dev_2.3.4-2 libmuparser2v5_2.3.4-2 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1 libnghttp2-14_1.68.0-2 libnghttp3-9_1.15.0-1 libngtcp2-16_1.21.0-1 libngtcp2-crypto-ossl0_1.21.0-1 libnl-3-200_3.12.0-2 libnl-3-dev_3.12.0-2 libnl-route-3-200_3.12.0-2 libnl-route-3-dev_3.12.0-2 libnuma-dev_2.0.19-1+b1 libnuma1_2.0.19-1+b1 libopenjp2-7_2.5.4-1 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpango-1.0-0_1.57.0-1 libpangocairo-1.0-0_1.57.0-1 libpangoft2-1.0-0_1.57.0-1 libpaper-utils_2.2.5-0.3+b3 libpaper2_2.2.5-0.3+b3 libpathplan4_14.1.2-1 libpciaccess0_0.17-3+b4 libpcre2-8-0_10.46-1+b1 libpdfbox-java_1:1.8.16-5 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2 libpixman-1-0_0.46.4-1+b1 libpkgconf7_2.5.1-4 libpmix2t64_6.0.0+really5.0.9-3 libpng16-16t64_1.6.55-1 libpotrace0_1.16-2+b3 libproc2-0_2:4.0.4-9+b1 libprrte-bin_3.0.13-2 libprrte-dev_3.0.13-2 libprrte3_3.0.13-2 libpsl5t64_0.21.2-1.1+b2 libpsm2-2_11.2.185-2.1 libptexenc1_2025.20250727.75242+ds-5+b2 libpython3-dev_3.13.9-3 libpython3-stdlib_3.13.9-3 libpython3.13_3.13.12-1 libpython3.13-dev_3.13.12-1 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 libquadmath0_16-20260308-1 librav1e0.8_0.8.1-7 librdmacm1t64_61.0-2 libreadline8t64_8.3-4 librhash1_1.4.6-1.1 librtmp1_2.4+20151223.gitfa8646d.1-3+b1 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsemanage-common_3.9-1 libsemanage2_3.9-1+b1 libsepol2_3.9-2 libsframe3_2.46-3 libsharpyuv0_1.5.0-0.1+b1 libsm6_2:1.2.6-1+b1 libsmartcols1_2.41.3-4 libspdlog1.15_1:1.15.3+ds-1+b1 libsqlite3-0_3.46.1-9+b1 libssh2-1t64_1.11.1-1+b1 libssl3t64_3.5.5-1 libstdc++-15-dev_15.2.0-15 libstdc++6_16-20260308-1 libsvtav1enc2_2.3.0+dfsg-1 libsynctex2_2025.20250727.75242+ds-5+b2 libsystemd-shared_260~rc2-1 libsystemd0_260~rc2-1 libtasn1-6_4.21.0-2 libteckit0_2.5.13+ds-1 libtexlua53-5_2025.20250727.75242+ds-5+b2 libtext-charwidth-perl_0.04-11+b5 libtext-wrapi18n-perl_0.06-10 libthai-data_0.1.30-1 libthai0_0.1.30-1 libtiff6_4.7.1-1 libtinfo6_6.6+20251231-1 libtool_2.5.4-9 libtsan2_16-20260308-1 libubsan1_16-20260308-1 libucc1_1.7.0~rc1-1 libuchardet0_0.0.8-2+b1 libucx0_1.20.0+ds-4 libudev1_260~rc2-1 libunistring5_1.4.2-1 libuuid1_2.41.3-4 libuv1t64_1.51.0-2+b1 libwebp7_1.5.0-0.1+b1 libwebpmux3_1.5.0-0.1+b1 libwmflite-0.2-7_0.2.14-1 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxapian30_1.4.31-2 libxau6_1:1.0.11-1+b1 libxaw7_2:1.0.16-1+b1 libxcb-render0_1.17.0-2+b2 libxcb-shm0_1.17.0-2+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2 libxdot4_14.1.2-1 libxext6_2:1.3.4-1+b4 libxi6_2:1.8.2-2 libxml2-16_2.15.1+dfsg-2+b1 libxmu6_2:1.1.3-4 libxnvctrl0_535.171.04-1+b3 libxpm4_1:3.5.17-1+b4 libxrender1_1:0.9.12-1+b1 libxt6t64_1:1.2.1-1.3+b1 libxxhash0_0.8.3-2+b1 libyuv0_0.0.1922.20260106-1 libz3-4_4.13.3-1+b1 libze1_1.28.2-1 libzstd1_1.5.7+dfsg-3+b1 libzzip-0-13t64_0.13.78+dfsg.1-0.2 linux-libc-dev_6.19.6-1 login.defs_1:4.19.3-1 lsb-release_12.1-2 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 mount_2.41.3-4 mpi-default-bin_1.20 mpi-default-dev_1.20 mscgen_0.20-16 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 netbase_6.5 ocl-icd-libopencl1_2.3.4-1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.2p1-5 openssl_3.5.5-1 openssl-provider-legacy_3.5.5-1 passwd_1:4.19.3-1 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 poppler-data_0.4.12-1 preview-latex-style_13.2-1.1 procps_2:4.0.4-9+b1 pybind11-dev_3.0.1-3 python-babel-localedata_2.17.0-2 python3_3.13.9-3 python3-accessible-pygments_0.0.5-2 python3-alabaster_1.0.0-1 python3-babel_2.17.0-2 python3-bs4_4.14.3-2 python3-certifi_2026.2.25+ds-1 python3-chardet_5.2.0+dfsg-2 python3-charset-normalizer_3.4.4-2 python3-defusedxml_0.7.1-3 python3-dev_3.13.9-3 python3-docutils_0.22.4+dfsg-1 python3-idna_3.11-1 python3-imagesize_1.4.1-1 python3-iniconfig_2.1.0-2 python3-jinja2_3.1.6-1 python3-markupsafe_3.0.3-1+b1 python3-minimal_3.13.9-3 python3-mpi4py_4.1.1-1+b1 python3-networkx_3.4.2-4 python3-numpy_1:2.3.5+ds-3 python3-numpy-dev_1:2.3.5+ds-3 python3-packaging_25.0-2 python3-pluggy_1.6.0-2 python3-pybind11_3.0.1-3 python3-pygments_2.19.2+dfsg-1 python3-pytest_9.0.2-4 python3-requests_2.32.5+dfsg-1 python3-roman-numerals_4.1.0-1 python3-snowballstemmer_3.0.1-1 python3-soupsieve_2.8.3-1 python3-sphinx_8.2.3-12 python3-sphinx-argparse_0.5.2-1 python3-sphinx-copybutton_0.5.2-3 python3-sphinx-inline-tabs_2023.4.21-3 python3-sphinxcontrib.autoprogram_0.1.9-1 python3-typing-extensions_4.15.0-2 python3-urllib3_2.6.3-1 python3.13_3.13.12-1 python3.13-dev_3.13.12-1 python3.13-minimal_3.13.12-1 rdfind_1.6.0-1+b1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.26 sgml-base_1.31+nmu1 sphinx-basic-ng_1.0.0~beta2-1 sphinx-common_8.2.3-12 symlinks_1.4-5+b1 systemd_260~rc2-1 sysvinit-utils_3.15-6 t1utils_1.41-4 tar_1.35+dfsg-4 tex-common_6.20 tex-gyre_20180621-7 texlive-base_2025.20260124-1 texlive-binaries_2025.20250727.75242+ds-5+b2 texlive-fonts-recommended_2025.20260124-1 texlive-latex-base_2025.20260124-1 texlive-latex-extra_2025.20260124-1 texlive-latex-recommended_2025.20260124-1 texlive-pictures_2025.20260124-1 tzdata_2026a-1 ucf_3.0052 util-linux_2.41.3-4 x11-common_1:7.7+26 xdg-utils_1.2.1-2 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+7 xml-core_0.19 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.1-3 zlib1g-dev_1:1.3.dfsg+really1.3.1-3 +------------------------------------------------------------------------------+ | Build Sat, 14 Mar 2026 05:54:29 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gromacs Binary: gromacs, gromacs-data, libgromacs11, libgromacs-dev, libnblib-gmx0, libnblib-gmx-dev Architecture: any all Version: 2026.1-1 Maintainer: Debichem Team Uploaders: Nicholas Breen Homepage: https://www.gromacs.org/ Standards-Version: 4.7.3 Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, mpi-default-bin, perl Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev Build-Depends-Indep: doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra Package-List: gromacs deb science optional arch=any gromacs-data deb science optional arch=all libgromacs-dev deb libdevel optional arch=any libgromacs11 deb libs optional arch=any libnblib-gmx-dev deb libdevel optional arch=any libnblib-gmx0 deb libs optional arch=any Checksums-Sha1: 38aed98a0a01adb50d5721d17b27bfa328db9376 16580717 gromacs_2026.1.orig-regressiontests.tar.gz 263dfd230007b0b2428f8b05fa5d96fad68786e5 45914061 gromacs_2026.1.orig.tar.gz d7d0d5e2eefb99d18d427675e13777e469a808b4 37208 gromacs_2026.1-1.debian.tar.xz Checksums-Sha256: dbdcc50bf1c1b590adeacfd5cf187f805bf4238aaf63cd05bb8958b49c1afd44 16580717 gromacs_2026.1.orig-regressiontests.tar.gz d95a313f56db7e05ee3a21e50f582fdee5176c2f60b900bab2461fd95c5e81be 45914061 gromacs_2026.1.orig.tar.gz 129934c052865fc9ebb7f684a865f792f49f9f24ae6a82ca64efac25ee846272 37208 gromacs_2026.1-1.debian.tar.xz Files: 20b6ff12cb489623f97154f98b9f17e1 16580717 gromacs_2026.1.orig-regressiontests.tar.gz 5e67383cea1093de10d89b807c448733 45914061 gromacs_2026.1.orig.tar.gz f92710a84f8d8880222ce36d72bc7074 37208 gromacs_2026.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmmsUzASHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCPHiMP/24eYHO3nZKbBmoK1g/QObPu2M8/h4IT QtgO9edT+F3y94SFgQYPIfJ+pqOH/+ENUCS/SXfAjIULXY8JxmHhCY7YKFxWB6Jj 0m2KCelzKSWQfPsY1vjq6BOwScKgobzAJ6/JpXwIi0FTe7gX1F6MHwqZ1ICUgd7Y FpeUY2LlYSuvrdj9tKHF0MnZhOXydZuI4+rGOVY75gUhXKgypXiu8y/vOyzKzBGH fyah6mdTEjEmjEciipliOrGIYvqvFFXxn9LxqneOcvjtfbit19/Dnwj4ALYolPdU e/oRQWq6vBQup21Z+gWrDubXf7m47+118gVJwoER1QAEs7toEg89gVEgBAkR6WkW usVaeqNfkz+X+itXZ2YzNB9qt3ID661mVQVjQHZFGftx8d/gZKlMniQQjgepvKUp pZ4CCNKJ40pCmpF0YjrcEE39//1Hy9P7u9iT+BnvFohaAQtKzYqWGXfs9/V/dfNk nhhKQD1EpJVlcBCAvU1/j6uWkya789DBMLWJa9rkFyO4wTmsnOdIJIAuHHeoBORN 5Jl0f6ottZ4k0VuLw9SUuU0AKCQUXLceXSwp0ECKgwbg2lzS08w70ymOdBIWz1gH 6kdv1zhPcJQ6jCQJ9cLm56qMSp039K3z1udZT38UbaiuledC9C5OONQ4yZvjsSsp +hM6jw6dp0UH =OcvM -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./gromacs_2026.1-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./gromacs_2026.1-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting gromacs in /build/reproducible-path/gromacs-2026.1 dpkg-source: info: unpacking gromacs_2026.1.orig.tar.gz dpkg-source: info: unpacking gromacs_2026.1.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2026.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying script-shebang-line.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1772897449 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -A dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2026.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary-indep dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2026.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel Xeon Processor (Skylake, IBRS) -- Detected build CPU family - 6 -- Detected build CPU model - 85 -- Detected build CPU stepping - 4 -- Detected build CPU features - aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (20.8s) -- Generating done (0.9s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.1/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2026.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel Xeon Processor (Skylake, IBRS) -- Detected build CPU family - 6 -- Detected build CPU model - 85 -- Detected build CPU stepping - 4 -- Detected build CPU features - aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (20.4s) -- Generating done (0.9s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.1/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2026.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.10 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel Xeon Processor (Skylake, IBRS) -- Detected build CPU family - 6 -- Detected build CPU model - 85 -- Detected build CPU stepping - 4 -- Detected build CPU features - aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO_AUTO -- Performing Test HAS_FLTO_AUTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2026.1/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "3.0.1") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.15.0") found components: doxygen dot -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (17.7s) -- Generating done (0.9s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.1/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2026.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.10 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel Xeon Processor (Skylake, IBRS) -- Detected build CPU family - 6 -- Detected build CPU model - 85 -- Detected build CPU stepping - 4 -- Detected build CPU features - aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.2.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (16.7s) -- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.1/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j6 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.1 -B/build/reproducible-path/gromacs-2026.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic/CMakeFiles /build/reproducible-path/gromacs-2026.1/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.1-Debian_2026.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.1/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.1-1 -P /build/reproducible-path/gromacs-2026.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/lmfit/lmmin.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/huffmem.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/collective.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/comm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/gather.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdpoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/xtc2.c /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/binary_information.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmforceproviderbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 4%] Built target thread_mpi cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 6%] Built target fmm cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 8%] Built target linearalgebra /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_histogram.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_histogram_reweight_amd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 10%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_meta.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md/h5md.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 10%] Built target h5md cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_restraint.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pullcoordexpressionparser.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 10%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/options.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsassigner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 10%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 10%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_apath.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 12%] Built target pulling cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_coordnums.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_distances.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 12%] Built target options cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/reportgpuusage.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/energydata.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 12%] Built target taskassignment cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvargrid_integrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/nosehooverchains.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/pullelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/trajectoryelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 16%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.1/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/veccompare.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/vecdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergykernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergykernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistsets.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistsets.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistsets.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistsets.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulesettings.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulesettings.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulesettings.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinemodulesettings.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/filenm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_zones.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/haloexchange.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/haloexchangesetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/serialization/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/serialization/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/serialization/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/serialization/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/serialization/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/serialization/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/external_tracing.cpp.o -MF CMakeFiles/libgromacs.dir/timing/external_tracing.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/external_tracing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/external_tracing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/embedded_system_preprocessing.cpp.o -MF CMakeFiles/libgromacs.dir/topology/embedded_system_preprocessing.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/embedded_system_preprocessing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/embedded_system_preprocessing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/compute_io.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/compute_io.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/expfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/integrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/histogram.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/frameconverters/register.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/dssp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/gyrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/isotope.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/msd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scatteringfactors.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/make_ndx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/pme_error.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs_constraint_group_sizes.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs_constraint_group_sizes.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs_constraint_group_sizes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/lincs_constraint_group_sizes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/correlationhistory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/histogramsize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceproviderstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceproviderstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceproviderstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmmforceproviderstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarssimulationsparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedOptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedOptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/plumedOptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/plumedMDModule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/nnpot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/nnpotforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/restcbt.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/fft/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/nvshmem_manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/gpu_utils_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -DGMX_SIMD_ENUM_VALUE="gmx::SimdType::X86_Sse4_1" -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/simd_support.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/plainpairlistranges.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/print_validation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdr_serializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdr_serializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdr_serializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xdr_serializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-soname,libgromacs.so.11 -o ../../lib/libgromacs.so.11.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.11.0.0 ../../lib/libgromacs.so.11 ../../lib/libgromacs.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/share/template /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/share/template /build/reproducible-path/gromacs-2026.1/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake "--color=" template make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" nblib make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/box.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/context.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT share/template/CMakeFiles/template.dir/template.cpp.o -MF CMakeFiles/template.dir/template.cpp.o.d -o CMakeFiles/template.dir/template.cpp.o -c /build/reproducible-path/gromacs-2026.1/share/template/template.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target gmx cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/template.dir/link.d CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 95%] Built target template cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" argon-forces-integration make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" methane-water-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/samples/methane-water-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.1/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.1/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -j6 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.1 -B/build/reproducible-path/gromacs-2026.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2026.1/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.1-Debian_2026.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.1/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.1-1 -P /build/reproducible-path/gromacs-2026.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/lmfit/lmmin.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 2%] Built target release-version-info cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/coder.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 2%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/fixpoint.c /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/huffman.c make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/collective.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/comm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/gather.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/xtc3.c [ 2%] Built target scanner /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 6%] Built target thread_mpi cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdpoptions.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmforceproviderbuilder.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/matrix.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmoptions.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md/h5md.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/abstractsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 8%] Built target linearalgebra cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_alb.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 8%] Built target h5md cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 10%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/behaviorcollection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 12%] Built target fmm /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_meta.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_opes.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 12%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/legacymodules.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/output.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 12%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pull_rotation.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pullcoordexpressionparser.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 12%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_angles.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 14%] Built target pulling cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/treesupport.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_apath.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/findallgputasks.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 14%] Built target options cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_neuralnetwork.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 14%] Built target taskassignment cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvargrid_integrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/nosehooverchains.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/pullelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 16%] Built target modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 20%] Built target colvars_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.1/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/veccompare.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/vecdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergykernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergykernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_simd_kernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistsets.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistsets.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistsets.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistsets.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulesettings.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulesettings.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulesettings.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlinemodulesettings.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/filenm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_zones.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/domdec_zones.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/haloexchange.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchangesetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/haloexchangesetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/serialization/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/serialization/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/serialization/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/serialization/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/serialization/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/serialization/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/external_tracing.cpp.o -MF CMakeFiles/libgromacs.dir/timing/external_tracing.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/external_tracing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/external_tracing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/embedded_system_preprocessing.cpp.o -MF CMakeFiles/libgromacs.dir/topology/embedded_system_preprocessing.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/embedded_system_preprocessing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/embedded_system_preprocessing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/compute_io.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/compute_io.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/expfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/integrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/histogram.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/frameconverters/register.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/frameconverters/register.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/dssp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/dssp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/gyrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/hbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/isotope.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/isotope.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/msd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scatteringfactors.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/scatteringfactors.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/make_ndx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/pme_error.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs_constraint_group_sizes.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs_constraint_group_sizes.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs_constraint_group_sizes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/lincs_constraint_group_sizes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/correlationhistory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/histogramsize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceproviderstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceproviderstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceproviderstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmmforceproviderstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarssimulationsparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarssimulationsparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedOptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedOptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/plumedOptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/plumed/plumedMDModule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/plumedMDModule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/nnpot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/nnpot/nnpotforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/nnpotforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/restcbt.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/fft/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/nvshmem_manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/gpu_utils_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -DGMX_SIMD_ENUM_VALUE="gmx::SimdType::X86_Sse4_1" -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/simd_support.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/simd_support.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/binary_information.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/binary_information.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/plainpairlistranges.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/print_validation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdr_serializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdr_serializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdr_serializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xdr_serializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-soname,libgromacs_d.so.11 -o ../../lib/libgromacs_d.so.11.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.11.0.0 ../../lib/libgromacs_d.so.11 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" gmx cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" nblib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/exceptions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/convertGmxToNblib.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" argon-forces-integration make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" methane-water-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/samples/argon-forces-integration.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.1/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.1/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -j6 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.1 -B/build/reproducible-path/gromacs-2026.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.1 -B/build/reproducible-path/gromacs-2026.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic/CMakeFiles 75 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" gtest make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.1-Debian_2026.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.1/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.1-1 -P /build/reproducible-path/gromacs-2026.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wundef -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-declarations -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 0%] Built target internal_rpc_xdr [ 0%] Built target scanner /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 2%] Built target tng_io_obj [ 2%] Built target mdrun_objlib [ 4%] Built target thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/fmm/CMakeFiles/fmm.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 4%] Built target lmfit_objlib [ 5%] Built target linearalgebra /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/DependInfo.cmake "--color=" mpithreads [ 6%] Built target fmm [ 6%] Built target options /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/depend /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/DependInfo.cmake "--color=" sync_cyclecount make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/DependInfo.cmake "--color=" mpi_speedtest [ 9%] Built target colvars_objlib /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test/CMakeFiles/notmpi.dir/DependInfo.cmake "--color=" notmpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/main.cpp.o -MF CMakeFiles/mpithreads.dir/main.cpp.o.d -o CMakeFiles/mpithreads.dir/main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -MF CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o.d -o CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/sync_cyclecount.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -MF CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/mpi_speedtest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/notmpi.dir/notmpi.cpp.o -MF CMakeFiles/notmpi.dir/notmpi.cpp.o.d -o CMakeFiles/notmpi.dir/notmpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/notmpi.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 9%] Built target h5md /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build.make src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/DependInfo.cmake "--color=" alloc_check cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -MF CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/send_recv.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build.make src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/notmpi.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/alloc_check.cpp.o -MF CMakeFiles/alloc_check.dir/alloc_check.cpp.o.d -o CMakeFiles/alloc_check.dir/alloc_check.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/alloc_check.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/reduce.cpp.o -MF CMakeFiles/mpithreads.dir/reduce.cpp.o.d -o CMakeFiles/mpithreads.dir/reduce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/reduce.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/sync_cyclecount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sync_cyclecount.dir/link.d CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/sync_cyclecount /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/notmpi.dir/link.d CMakeFiles/notmpi.dir/notmpi.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/notmpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 9%] Built target sync_cyclecount /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling [ 9%] Built target notmpi cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -MF CMakeFiles/mpi_speedtest.dir/multicast.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/multicast.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 10%] Built target pulling /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/once.cpp.o -MF CMakeFiles/mpithreads.dir/once.cpp.o.d -o CMakeFiles/mpithreads.dir/once.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/once.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/send_recv.cpp.o -MF CMakeFiles/mpithreads.dir/send_recv.cpp.o.d -o CMakeFiles/mpithreads.dir/send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/send_recv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/alloc_check.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alloc_check.dir/link.d CMakeFiles/alloc_check.dir/alloc_check.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/alloc_check make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 10%] Built target alloc_check /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpi_speedtest.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator [ 10%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/multicast.cpp.o -MF CMakeFiles/mpithreads.dir/multicast.cpp.o.d -o CMakeFiles/mpithreads.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cond-var.cpp.o -MF CMakeFiles/mpithreads.dir/cond-var.cpp.o.d -o CMakeFiles/mpithreads.dir/cond-var.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/cond-var.cpp [ 10%] Built target taskassignment cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/atomic.cpp.o -MF CMakeFiles/mpithreads.dir/atomic.cpp.o.d -o CMakeFiles/mpithreads.dir/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/atomic.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpi_speedtest.dir/link.d CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpi_speedtest make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 12%] Built target mpi_speedtest cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cycles.cpp.o -MF CMakeFiles/mpithreads.dir/cycles.cpp.o.d -o CMakeFiles/mpithreads.dir/cycles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/cycles.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 13%] Built target modularsimulator cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/split.cpp.o -MF CMakeFiles/mpithreads.dir/split.cpp.o.d -o CMakeFiles/mpithreads.dir/split.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/split.cpp /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpithreads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpithreads.dir/link.d CMakeFiles/mpithreads.dir/main.cpp.o CMakeFiles/mpithreads.dir/reduce.cpp.o CMakeFiles/mpithreads.dir/once.cpp.o CMakeFiles/mpithreads.dir/send_recv.cpp.o CMakeFiles/mpithreads.dir/multicast.cpp.o "CMakeFiles/mpithreads.dir/cond-var.cpp.o" CMakeFiles/mpithreads.dir/atomic.cpp.o CMakeFiles/mpithreads.dir/cycles.cpp.o CMakeFiles/mpithreads.dir/split.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpithreads make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 13%] Built target mpithreads make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 62%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" nblib make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 64%] Built target gmxapi [ 65%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" argon-forces-integration make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" methane-water-integration make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 65%] Built target argon-forces-integration [ 65%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-soname,libgtest.so.1.17.0 -o ../../../../lib/libgtest.so.1.17.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 65%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googlemock /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" gmock make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wundef -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmock.dir/link.d -Wl,-soname,libgmock.so.1.17.0 -o ../../../../lib/libgmock.so.1.17.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.17.0 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 65%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/testutils /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake "--color=" testutils make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/conftest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/filematchers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o -MF CMakeFiles/testutils.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/interactivetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o -MF CMakeFiles/testutils.dir/loggertest.cpp.o.d -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/loggertest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o -MF CMakeFiles/testutils.dir/mpi_printer.cpp.o.d -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/mpi_printer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o -MF CMakeFiles/testutils.dir/mpitest.cpp.o.d -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/mpitest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DHAVE_OPEN_MEMSTREAM=1 -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/posixmemstream.cpp.o -MF CMakeFiles/testutils.dir/posixmemstream.cpp.o.d -o CMakeFiles/testutils.dir/posixmemstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/posixmemstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o -MF CMakeFiles/testutils.dir/refdata.cpp.o.d -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/refdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o -MF CMakeFiles/testutils.dir/refdata_xml.cpp.o.d -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/refdata_xml.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/setenv.cpp.o -MF CMakeFiles/testutils.dir/setenv.cpp.o.d -o CMakeFiles/testutils.dir/setenv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/setenv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o -MF CMakeFiles/testutils.dir/simulationdatabase.cpp.o.d -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o -MF CMakeFiles/testutils.dir/stdiohelper.cpp.o.d -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/stdiohelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o -MF CMakeFiles/testutils.dir/stringtest.cpp.o.d -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/stringtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o -MF CMakeFiles/testutils.dir/testasserts.cpp.o.d -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testasserts.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o -MF CMakeFiles/testutils.dir/testfilemanager.cpp.o.d -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testfilemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o -MF CMakeFiles/testutils.dir/testfileredirector.cpp.o.d -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testfileredirector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o -MF CMakeFiles/testutils.dir/test_device.cpp.o.d -o CMakeFiles/testutils.dir/test_device.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/test_device.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -MF CMakeFiles/testutils.dir/test_hardware_environment.cpp.o.d -o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/test_hardware_environment.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o -MF CMakeFiles/testutils.dir/testinit.cpp.o.d -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testinit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o -MF CMakeFiles/testutils.dir/testmatchers.cpp.o.d -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testmatchers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o -MF CMakeFiles/testutils.dir/testoptions.cpp.o.d -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o -MF CMakeFiles/testutils.dir/textblockmatchers.cpp.o.d -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/textblockmatchers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/topologyhelpers.cpp.o -MF CMakeFiles/testutils.dir/topologyhelpers.cpp.o.d -o CMakeFiles/testutils.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -MF CMakeFiles/testutils.dir/tprfilegenerator.cpp.o.d -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tprfilegenerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/trajectoryreader.cpp.o -MF CMakeFiles/testutils.dir/trajectoryreader.cpp.o.d -o CMakeFiles/testutils.dir/trajectoryreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/trajectoryreader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o -MF CMakeFiles/testutils.dir/xvgtest.cpp.o.d -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/xvgtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -MF CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o.d -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2/tinyxml2.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/posixmemstream.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/setenv.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/topologyhelpers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/trajectoryreader.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 66%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake "--color=" mdrun_test_infrastructure make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake "--color=" nblib_test_infrastructure make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake "--color=" testutils-mpi-test make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake "--color=" testutils-test make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/DependInfo.cmake "--color=" mpicomm-test make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake "--color=" utility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/interactivetest.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/energyreader.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/testsystems.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/mpitest.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o -MF CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o.d -o CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/naming.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 66%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpicomm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpicomm-test.dir/link.d "CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o" "CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mpicomm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 66%] Built target mpicomm-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/posixmemstream.cpp.o -MF CMakeFiles/testutils-test.dir/posixmemstream.cpp.o.d -o CMakeFiles/testutils-test.dir/posixmemstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/posixmemstream.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" utility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o -MF CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/coordinate_exception_handling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/arrayref.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" mdlib-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 66%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o" "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 66%] Built target utility-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constr.cpp /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 68%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -MF CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o.d -o CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constraintgroupsize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/posixmemstream.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 68%] Built target testutils-test /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" density_fitting_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" qmmm_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/energyoutput.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" colvars_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 68%] Built target density_fitting_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmforceproviderstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" plumed_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/logger.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 68%] Built target qmmm_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 68%] Built target plumed_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 68%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 69%] Built target awh-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mpicomm.cpp.o -MF CMakeFiles/utility-test.dir/mpicomm.cpp.o.d -o CMakeFiles/utility-test.dir/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/mpicomm.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" plumed_md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/path.cpp /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" nnpot_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" listed_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 69%] Built target plumed_md-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" nbnxm-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/scope_guard.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 69%] Built target applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests/pairs.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" nbnxm-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 69%] Built target nbnxm-gpu-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 70%] Built target nnpot_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/simulationsignal.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" nonbonded-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -MF CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o.d -o CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/plainpairlist.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 70%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/DependInfo.cmake "--color=" nonbonded-fep-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/freeenergygpukernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-gpu-test.dir/link.d "CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o" "CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 70%] Built target nonbonded-fep-gpu-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/testsystem.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" onlinehelp-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/vsite.cpp.o -MF CMakeFiles/mdlib-test.dir/vsite.cpp.o.d -o CMakeFiles/mdlib-test.dir/vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/txtdump.cpp.o -MF CMakeFiles/utility-test.dir/txtdump.cpp.o.d -o CMakeFiles/utility-test.dir/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/txtdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" domdec-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests/hashedmap.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp [ 70%] Built target nbnxm-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 70%] Built target nonbonded-fep-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 70%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" domdec-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vecdump.cpp.o -MF CMakeFiles/utility-test.dir/vecdump.cpp.o.d -o CMakeFiles/utility-test.dir/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/vecdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vectypes.cpp.o -MF CMakeFiles/utility-test.dir/vectypes.cpp.o.d -o CMakeFiles/utility-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 70%] Built target domdec-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" ewald-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmebsplinetest.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/vsite.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 72%] Built target mdlib-test /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/DependInfo.cmake "--color=" fmm-interface-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmm_mdpoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 72%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmesolvetest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/mpicomm.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/txtdump.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/vecdump.cpp.o" "CMakeFiles/utility-test.dir/vectypes.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 73%] Built target utility-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmm_mdpvalidator.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 73%] Built target fft-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/DependInfo.cmake "--color=" gpu_utils-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o -MF CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o.d -o CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmmforceproviderbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/hostallocator.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/typecasts.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-mpi-test.dir/link.d "CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o" "CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 73%] Built target gpu_utils-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fmm-interface-tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fmm-interface-tests.dir/link.d "CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o" "CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fmm-interface-tests ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 73%] Built target fmm-interface-tests cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/complex.cpp /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 74%] Built target ewald-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" mdtypes-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 74%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 74%] Built target hardware-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 74%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 74%] Built target onlinehelp-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/densityfittingforce.cpp /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" options-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 74%] Built target mdspan-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/multidimarray.cpp /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/neldermead.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/pbc.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 76%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/DependInfo.cmake "--color=" serialization-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/seed.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 76%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 77%] Built target mdtypes-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/serialization-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/serialization-test.dir/link.d "CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/serialization-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 77%] Built target serialization-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/treesupport.cpp /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 77%] Built target random-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" timing-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 77%] Built target timing-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 77%] Built target taskassignment-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 78%] Built target math-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 78%] Built target table-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 78%] Built target pull-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/generate_test_points.cpp.o -MF CMakeFiles/simd-test.dir/generate_test_points.cpp.o.d -o CMakeFiles/simd-test.dir/generate_test_points.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/generate_test_points.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/entropy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 80%] Built target options-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/mtop.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 80%] Built target compat-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -MF CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmxanatestbase.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/symtab.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rmsdist.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 81%] Built target topology-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 81%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 81%] Built target pdb2gmx2-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 82%] Built target gmxana-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_vector_operations.cpp /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" correlations-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" analysisdata-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 84%] Built target pdb2gmx3-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/builder.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 85%] Built target correlations-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/generate_test_points.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 86%] Built target simd-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/register.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" tool-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/settimestep.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target analysisdata-test-shared /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" tool-test-with-leaks make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/report_methods.cpp /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/DependInfo.cmake "--color=" h5md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o -MF CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o.d -o CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md/tests/h5md_disabled.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/confio.cpp /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/h5md-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/h5md-test.dir/link.d "CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o" "CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/h5md.dir/h5md.cpp.o -o ../../../../../bin/h5md-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target h5md-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/nbsearch.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/filetypes.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/matio.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" mdrun-output-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/selectioncollection.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target tool-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/readinp.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/interactiveMD.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/awh.cpp.o -MF CMakeFiles/mdrun-test.dir/awh.cpp.o.d -o CMakeFiles/mdrun-test.dir/awh.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/awh.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/timecontrol.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target selection-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -MF CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o.d -o CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/xdr_serializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" mdrun-single-rank-algorithms-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/initialconstraints.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" minimize-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/termination.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/freezegroups.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 88%] Built target fileio-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 89%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/tpitest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 89%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" mdrun-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 89%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" mdrun-multisim-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 89%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/boxdeformation.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/replicaexchange.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp [ 89%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-equivalence-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/awh.cpp.o" "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 89%] Built target mdrun-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/replicaexchange_equivalence.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 89%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" mdrun-mpi-pme-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 90%] Built target mdrun-non-integrator-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" mdrun-coordination-basic-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" mdrun-coordination-coupling-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 90%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" mdrun-coordination-constraints-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 92%] Built target mdrun-mpi-pme-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions_constraints.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 92%] Built target mdrun-coordination-basic-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" mdrun-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/expandedensemble.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" mdrun-pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 92%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" mdrun-rotation-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" mdrun-simulator-comparison-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/simulator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" mdrun-vsites-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/virtualsites.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" gmxapi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/restraint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" workflow-details-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target mdrun-rotation-test cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 93%] Built target mdrun-vsites-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" nblib-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 94%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" nblib-setup-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 94%] Built target mdrun-pull-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" nblib-tpr-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/molecules.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" nblib-integration-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 94%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 96%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" nblib-listed-forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 96%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/kernels.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 96%] Built target nblib-integration-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/util/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" nblib-util-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 96%] Built target nblib-util-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/shiftforces.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -MF CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/plainpairlistranges.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 96%] Built target nblib-setup-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" analysisdata-test /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/analysisdata.cpp [ 97%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 97%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/filenm.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 97%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/average.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" nblib-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/dssp.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 98%] Built target commandline-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [ 98%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' cd /build/reproducible-path/gromacs-2026.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic /build/reproducible-path/gromacs-2026.1/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.1/build/basic/lib ctest -V ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2026.1/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2026.1/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2026.1/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -67183395 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.028 0.014 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 36.540 0.657 4.618 0.002 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (255 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1872680351 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.022 0.011 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 46.773 0.513 3.608 0.002 1: [ OK ] GmxApiTest.RunnerBasicMD (236 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -86573290 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.021 0.011 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 333.010 0.072 0.507 0.016 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.022 0.011 199.3 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 328.455 0.073 0.514 0.016 1: [ OK ] GmxApiTest.RunnerReinitialize (249 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 535756094 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.020 0.010 198.6 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 49.940 0.481 3.379 0.002 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.020 0.010 199.2 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 50.694 0.473 3.329 0.002 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (248 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -439664673 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.017 0.009 198.7 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 96.915 0.248 1.741 0.005 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.018 0.009 199.0 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 36.444 0.659 4.630 0.002 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (256 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -1075069442 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (204 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (1450 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (1467 ms total) 1: [ PASSED ] 9 tests. 1/104 Test #1: GmxapiExternalInterfaceTests .............. Passed 1.48 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 2000670682 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (212 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -18876705 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (189 ms) 2: [----------] 2 tests from GmxApiTest (402 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (416 ms total) 2: [ PASSED ] 2 tests. 2/104 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.43 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (18 ms) 3: [----------] 8 tests from NBlibTest (19 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (0 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (0 ms) 3: [----------] 1 test from LinearChainDataFixture (0 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (22 ms total) 3: [ PASSED ] 44 tests. 3/104 Test #3: NbLibListedForcesTests .................... Passed 0.03 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/104 Test #4: NbLibSamplesTestArgon ..................... Passed 0.01 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 5/104 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.01 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/104 Test #6: NbLibUtilTests ............................ Passed 0.01 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (1 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (1 ms total) 7: [ PASSED ] 57 tests. 7/104 Test #7: NbLibSetupTests ........................... Passed 0.03 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (4 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (3 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (4 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (4 ms) 8: [----------] 4 tests from TprReaderTest (16 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (30 ms total) 8: [ PASSED ] 4 tests. 8/104 Test #8: NbLibTprTests ............................. Passed 0.04 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (4 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (4 ms total) 9: [ PASSED ] 20 tests. 9/104 Test #9: NbLibIntegrationTests ..................... Passed 0.02 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/104 Test #10: NbLibIntegratorTests ...................... Passed 0.01 sec test 11 Start 11: threadMPI-mpithreads 11: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mpithreads "-nt" "3" 11: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test 11: Test timeout computed to be: 1500 11: 11: thread_mpi tester. 11: 11: Number of threads: 3 11: 11: thread 2: got arg 10; total number of hw threads: 16 11: my rank = 2 11: thread 0: got arg 10; total number of hw threads: 16 11: thread 1: got arg 10; total number of hw threads: 16 11: my rank = 0 11: my rank = 1 11: Setting thread affinity 11: Testing atomic functions.. 11: OK. 11: Starting tMPI_Thread_cond_signal test: 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 1: 501 11: processed by thread 2: 499 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 503 11: processed by thread 2: 497 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 429 11: processed by thread 1: 571 11: 11: Starting tMPI_Thread_cond_broadcast test: 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 1: 692 11: processed by thread 2: 1308 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 1190 11: processed by thread 2: 810 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 1189 11: processed by thread 1: 811 11: 11: 11: sizeof(atomic_t) = 64, sizeof(atomic_t_ptr)=64, sizeof(spinlock)=64 11: Testing spinlocks.. 11: OK. 11: 11: Testing locks.. 11: OK. 11: 11: Barrier data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Starting MPI_Send and MPI_Recv tests 11: Received: 'From thread 1 to 0: hello.' 11: Received: 'From thread 2 to 0: hello.' 11: Received: 'From thread 1 to 1: hello.' 11: Received: 'From thread 2 to 1: hello.' 11: 11: Starting MPI_Sendrecv tests 11: Received: 'Sendrecv hello, from thread 1' 11: Received: 'Sendrecv hello, from thread 2' 11: Received: 'Sendrecv hello, from thread 0' 11: 11: Starting MPI_Isend/MPI_Irecv tests 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Split test 11: I'm in world rank 1, and have new rank 0 in group 0x7f4750008960 of size 1 11: I'm in world rank 0, and have new rank 1 in group 0x7f4750007b00 of size 2 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0x7f4750007b00 of size 2 11: I'm in world rank 1, and have new rank 0 in group 0x7f4750009350 of size 1 11: my rank is 1, MPI_Comm_compare said: 3 11: I'm in world rank 2, and have new rank 0 in group 0x7f4750009c10 of size 1 11: my rank is 2, MPI_Comm_compare said: 3 11: I'm in world rank 0, and have new rank 0 in group 0x7f4750008960 of size 1 11: my rank is 0, MPI_Comm_compare said: 3 11: 11: Starting MPI_Split test 11: I'm in world rank 1, and have new rank 1 in group 0x7f4750009350 of size 3 11: my rank is 1, MPI_Comm_compare said: 2 11: I'm in world rank 2, and have new rank 0 in group 0x7f4750009350 of size 3 11: my rank is 2, MPI_Comm_compare said: 2 11: I'm in world rank 0, and have new rank 2 in group 0x7f4750009350 of size 3 11: my rank is 0, MPI_Comm_compare said: 2 11: Starting repeated MPI_Split() test. 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: Done. 11: 11: Starting MPI_Bcast test 11: Received: 'Broadcast message 0 from 0' 11: Received: 'Broadcast message 0 from 1' 11: Received: 'Broadcast message 0 from 2' 11: Received: 'Broadcast message 1 from 0' 11: Received: 'Broadcast message 1 from 1' 11: Received: 'Broadcast message 1 from 2' 11: Broadcast data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Gather test 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Gather data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Gatherv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Scatter test 11: Received from 0: 'Scatter message from 000 to 000' 11: Received back from 1: 'Scatter message from 000 to 001' 11: Received back from 2: 'Scatter message from 000 to 002' 11: Scatter data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Scatterv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Alltoall test 11: From 0: 0->0(0) 1->0(0) 2->0(0) 11: From 1: 0->1(0) 1->1(0) 2->1(0) 11: From 2: 0->2(0) 1->2(0) 2->2(0) 11: From 0: 0->0(1) 1->0(1) 2->0(1) 11: From 1: 0->1(1) 1->1(1) 2->1(1) 11: From 2: 0->2(1) 1->2(1) 2->2(1) 11: From 0: 0->0(2) 1->0(2) 2->0(2) 11: From 1: 0->1(2) 1->1(2) 2->1(2) 11: From 2: 0->2(2) 1->2(2) 2->2(2) 11: From 0: 0->0(3) 1->0(3) 2->0(3) 11: From 1: 0->1(3) 1->1(3) 2->1(3) 11: From 2: 0->2(3) 1->2(3) 2->2(3) 11: Alltoallv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Reduce test 11: again: my rank = 0 11: again: my rank = 2 11: Results from mpi_reduce: 11: (0: 2 == 2): OK 11: (1: 5 == 5): OK 11: (2: 8 == 8): OK 11: (3: 11 == 11): OK 11: (4: 14 == 14): OK 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 1 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 1: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 2: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 1: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 2: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Scan test 11: Results from mpi_scan process 0: 11: OK 11: again: my rank = 0 11: again: my rank = 1 11: again: my rank = 2 11: 11: Starting tMPI_Once test 11: Printing this number once: 0 (my rank=2) 11: Printing this number once: 2 (my rank=0) 11: Printing this number once: 3 (my rank=0) 11: I was first for 0, my rank=2 11: Printing this number once: 4 (my rank=2) 11: Printing this number once: 5 (my rank=2) 11: Printing this number once: 6 (my rank=0) 11: Printing this number once: 7 (my rank=0) 11: Printing this number once: 8 (my rank=2) 11: Printing this number once: 9 (my rank=2) 11: Printing this number once: 1 (my rank=1) 11: Done. 11: 11: Finishing.. 11/104 Test #11: threadMPI-mpithreads ...................... Passed 11.00 sec test 12 Start 12: threadMPI-sync_cyclecount 12: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/sync_cyclecount "2" "0" "1" 12: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test 12: Test timeout computed to be: 1500 12: 12: sync_cyclecount. 12: 12: Number of threads: 3 12: 12: Number of counters: 3 12: 12: No cycle count. 12/104 Test #12: threadMPI-sync_cyclecount ................. Passed 0.00 sec test 13 Start 13: threadMPI-mpi_speedtest 13: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mpi_speedtest "-nt" "3" 13: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test 13: Test timeout computed to be: 1500 13: Starting Thread 2: 13: Starting Thread 0: 13: Async data test: 13: Starting Thread 1: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Broadcast data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Gather data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Scatter data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Scatterv data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Alltoallv data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>Thread 2: 1.65687e+10 cycles 13: Thread 1: 1.65686e+10 cycles 13: 13: OK. 13: Thread 0: 1.65687e+10 cycles 13/104 Test #13: threadMPI-mpi_speedtest ................... Passed 7.89 sec test 14 Start 14: threadMPI-notmpi 14: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/notmpi "-nt" "3" 14: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test 14: Test timeout computed to be: 1500 14: 14: notmpi. 14: 14: Number of threads: 3 14: 14: This platform supports setting thread affinity 14: My ID=0, i=1000, tid=0x55a6a13e85f0 14: My ID=1, i=1000, tid=0x7f90f0000be0 14: My ID=2, i=1000, tid=0x7f90e8000be0 14: Total count: 3000 14/104 Test #14: threadMPI-notmpi .......................... Passed 0.00 sec test 15 Start 15: threadMPI-alloc_check 15: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/alloc_check "-nt" "3" 15: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/external/thread_mpi/test 15: Test timeout computed to be: 1500 15: 15: Memory (de)allocation tester. 15: 15: Number of threads: 3 15: 15: thread 2: got arg 10; total number of hw threads: 16 15: my rank = 2 15: thread 0: got arg 10; total number of hw threads: 16 15: my rank = 0 15: thread 1: got arg 10; total number of hw threads: 16 15: my rank = 1 15: 15: Starting MPI_Sendrecv tests 15: Received: 'Sendrecv hello, from thread 1' 15: Received: 'Sendrecv hello, from thread 2' 15: Received: 'Sendrecv hello, from thread 0' 15: 15: Starting MPI_Bcast test 15: Received: 'Broadcast message 0 from 0' 15: Received: 'Broadcast message 0 from 1' 15: Received: 'Broadcast message 0 from 2' 15: Received: 'Broadcast message 1 from 0' 15: Received: 'Broadcast message 1 from 1' 15: Received: 'Broadcast message 1 from 2' 15: 15: Starting MPI_Gather test 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Finishing.. 15/104 Test #15: threadMPI-alloc_check ..................... Passed 0.00 sec test 16 Start 16: TestUtilsUnitTests 16: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests 16: Test timeout computed to be: 30 16: [==========] Running 81 tests from 8 test suites. 16: [----------] Global test environment set-up. 16: [----------] 10 tests from InteractiveTestHelperTest 16: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 16: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 16: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 16: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 16: 16: [----------] 10 tests from NameOfTestFromTupleTest 16: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 16: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 16: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 16: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 16: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 16: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 16: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 16: 16: [----------] 3 tests from RefDataFilenameMakerTest 16: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 16: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 16: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 16: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 16: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 16: 16: [----------] 6 tests from PosixMemstreamTest 16: [ RUN ] PosixMemstreamTest.ConstructsAndDestructs 16: [ OK ] PosixMemstreamTest.ConstructsAndDestructs (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilClosed 16: [ OK ] PosixMemstreamTest.HasAStreamUntilClosed (0 ms) 16: [ RUN ] PosixMemstreamTest.CanFetchString 16: [ OK ] PosixMemstreamTest.CanFetchString (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilStringIsFetched 16: [ OK ] PosixMemstreamTest.HasAStreamUntilStringIsFetched (0 ms) 16: [ RUN ] PosixMemstreamTest.CanWriteToStream 16: [ OK ] PosixMemstreamTest.CanWriteToStream (0 ms) 16: [ RUN ] PosixMemstreamTest.CanCheckBufferWithContents 16: [ OK ] PosixMemstreamTest.CanCheckBufferWithContents (0 ms) 16: [----------] 6 tests from PosixMemstreamTest (0 ms total) 16: 16: [----------] 37 tests from ReferenceDataTest 16: [ RUN ] ReferenceDataTest.HandlesSimpleData 16: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 16: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 16: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringBlockData 16: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesVectorData 16: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceData 16: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectData 16: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 16: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingData 16: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedData 16: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnys 16: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 16: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 16: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 16: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 16: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 16: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 16: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 16: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 16: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesReadingValues 16: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 16: [----------] 37 tests from ReferenceDataTest (4 ms total) 16: 16: [----------] 7 tests from FloatingPointDifferenceTest 16: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 16: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 16: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 16: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 16: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 16: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 16: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 16: 16: [----------] 4 tests from FloatingPointToleranceTest 16: [ RUN ] FloatingPointToleranceTest.UlpTolerance 16: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 16: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 16: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 16: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 16: 16: [----------] 4 tests from XvgTests 16: [ RUN ] XvgTests.CreateFile 16: [ OK ] XvgTests.CreateFile (0 ms) 16: [ RUN ] XvgTests.CheckMissing 16: [ OK ] XvgTests.CheckMissing (0 ms) 16: [ RUN ] XvgTests.CheckExtra 16: [ OK ] XvgTests.CheckExtra (0 ms) 16: [ RUN ] XvgTests.ReadIncorrect 16: [ OK ] XvgTests.ReadIncorrect (0 ms) 16: [----------] 4 tests from XvgTests (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 81 tests from 8 test suites ran. (7 ms total) 16: [ PASSED ] 81 tests. 16/104 Test #16: TestUtilsUnitTests ........................ Passed 0.02 sec test 17 Start 17: TestUtilsMpiUnitTests 17: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/testutils/tests 17: Test timeout computed to be: 30 17: [==========] Running 3 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 1 test from MpiSelfTest 17: [ RUN ] MpiSelfTest.Runs 17: [ OK ] MpiSelfTest.Runs (0 ms) 17: [----------] 1 test from MpiSelfTest (0 ms total) 17: 17: [----------] 2 tests from MpiRefDataTest 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank (0 ms) 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName (0 ms) 17: [----------] 2 tests from MpiRefDataTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 3 tests from 2 test suites ran. (1 ms total) 17: [ PASSED ] 3 tests. 17/104 Test #17: TestUtilsMpiUnitTests ..................... Passed 0.01 sec test 18 Start 18: UtilityUnitTests 18: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/UtilityUnitTests.xml" 18: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests 18: Test timeout computed to be: 30 18: [==========] Running 495 tests from 68 test suites. 18: [----------] Global test environment set-up. 18: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/0.Comparison 18: [ OK ] AllocatorTest/0.Comparison (0 ms) 18: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.Move 18: [ OK ] AllocatorTest/0.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/0 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/1.Comparison 18: [ OK ] AllocatorTest/1.Comparison (0 ms) 18: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.Move 18: [ OK ] AllocatorTest/1.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/1 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/2.Comparison 18: [ OK ] AllocatorTest/2.Comparison (0 ms) 18: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.Move 18: [ OK ] AllocatorTest/2.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/2 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/3.Comparison 18: [ OK ] AllocatorTest/3.Comparison (0 ms) 18: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.Move 18: [ OK ] AllocatorTest/3.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/3 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/4.Comparison 18: [ OK ] AllocatorTest/4.Comparison (0 ms) 18: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.Move 18: [ OK ] AllocatorTest/4.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/4 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator,gmx::PageAlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/5.Comparison 18: [ OK ] AllocatorTest/5.Comparison (0 ms) 18: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.Move 18: [ OK ] AllocatorTest/5.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/5 (0 ms total) 18: 18: [----------] 1 test from AllocatorUntypedTest 18: [ RUN ] AllocatorUntypedTest.Comparison 18: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 18: [----------] 1 test from AllocatorUntypedTest (0 ms total) 18: 18: [----------] 4 tests from EmptyArrayRefTest 18: [ RUN ] EmptyArrayRefTest.IsEmpty 18: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 18: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 18: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 18: 18: [----------] 1 test from EmptyConstArrayRefTest 18: [ RUN ] EmptyConstArrayRefTest.IsEmpty 18: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 18: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 18: 18: [----------] 8 tests from BoolType 18: [ RUN ] BoolType.ImplicitConversion 18: [ OK ] BoolType.ImplicitConversion (0 ms) 18: [ RUN ] BoolType.FalseByDefault 18: [ OK ] BoolType.FalseByDefault (0 ms) 18: [ RUN ] BoolType.Assignment 18: [ OK ] BoolType.Assignment (0 ms) 18: [ RUN ] BoolType.Copy 18: [ OK ] BoolType.Copy (0 ms) 18: [ RUN ] BoolType.ArrayRefCanBeCreated 18: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 18: [ RUN ] BoolType.CanBeCastToBool 18: [ OK ] BoolType.CanBeCastToBool (0 ms) 18: [ RUN ] BoolType.HasSizeOfBool 18: [ OK ] BoolType.HasSizeOfBool (0 ms) 18: [ RUN ] BoolType.HasAlignmentOfBool 18: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 18: [----------] 8 tests from BoolType (0 ms total) 18: 18: [----------] 4 tests from ArrayRefFromBoolTypeVector 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.Works 18: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 18: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 18: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 18: 18: [----------] 7 tests from CStringUtilityTest 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 18: [ RUN ] CStringUtilityTest.strip_comment 18: [ OK ] CStringUtilityTest.strip_comment (0 ms) 18: [ RUN ] CStringUtilityTest.upstring 18: [ OK ] CStringUtilityTest.upstring (0 ms) 18: [ RUN ] CStringUtilityTest.ltrim 18: [ OK ] CStringUtilityTest.ltrim (0 ms) 18: [ RUN ] CStringUtilityTest.rtrim 18: [ OK ] CStringUtilityTest.rtrim (0 ms) 18: [ RUN ] CStringUtilityTest.trim 18: [ OK ] CStringUtilityTest.trim (0 ms) 18: [----------] 7 tests from CStringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from DefaultInitializationAllocator 18: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 18: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 18: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 18: 18: [----------] 4 tests from EnumerationHelpersTest 18: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 18: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 18: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 18: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 18: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 18: 18: [----------] 1 test from EnumClassSuitsEnumerationArray 18: [ RUN ] EnumClassSuitsEnumerationArray.Works 18: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 18: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 18: 18: [----------] 18 tests from FixedCapacityVectorTest 18: [ RUN ] FixedCapacityVectorTest.IsEmpty 18: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 18: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PushWorks 18: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PopWorks 18: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ResizeWorks 18: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ClearWorks 18: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 18: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.AtThrows 18: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 18: [ RUN ] FixedCapacityVectorTest.IteratorWorks 18: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 18: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 18: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 18: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 18: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.DataWorks 18: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 18: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 18: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 18: 18: [----------] 7 tests from TreeValueTransformTest 18: [ RUN ] TreeValueTransformTest.SimpleTransforms 18: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 18: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 18: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromString 18: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 18: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 18: [ RUN ] TreeValueTransformTest.ScopedTransformRules 18: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 18: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 18: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 18: [----------] 7 tests from TreeValueTransformTest (0 ms total) 18: 18: [----------] 1 test from TreeValueTransformErrorTest 18: [ RUN ] TreeValueTransformErrorTest.ConversionError 18: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 18: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 18: 18: [----------] 9 tests from ListOfLists 18: [ RUN ] ListOfLists.EmptyListOfListsWorks 18: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 18: [ RUN ] ListOfLists.AppendWorks 18: [ OK ] ListOfLists.AppendWorks (0 ms) 18: [ RUN ] ListOfLists.EmptyListWorks 18: [ OK ] ListOfLists.EmptyListWorks (0 ms) 18: [ RUN ] ListOfLists.AppendAccessWorks 18: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 18: [ RUN ] ListOfLists.ClearWorks 18: [ OK ] ListOfLists.ClearWorks (0 ms) 18: [ RUN ] ListOfLists.OutOfRangeAccessThrows 18: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 18: [ RUN ] ListOfLists.FrontAndBackWork 18: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 18: [ RUN ] ListOfLists.ExtractsAndRestores 18: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 18: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 18: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 18: [----------] 9 tests from ListOfLists (0 ms total) 18: 18: [----------] 7 tests from LoggerTest 18: [ RUN ] LoggerTest.EmptyLoggerWorks 18: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToStream 18: [ OK ] LoggerTest.LogsToStream (0 ms) 18: [ RUN ] LoggerTest.LogsToFile 18: [ OK ] LoggerTest.LogsToFile (0 ms) 18: [ RUN ] LoggerTest.LevelFilteringWorks 18: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleStreams 18: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleFiles 18: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 18: [ RUN ] LoggerTest.LogsToStreamAndFile 18: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 18: [----------] 7 tests from LoggerTest (0 ms total) 18: 18: [----------] 7 tests from MessageStringCollectorTest 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 18: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 18: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveAssign 18: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 18: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 18: 18: [----------] 12 tests from MpiComm 18: [ RUN ] MpiComm.SingleRankNoComm 18: [ OK ] MpiComm.SingleRankNoComm (0 ms) 18: [ RUN ] MpiComm.CommWorld 18: [ OK ] MpiComm.CommWorld (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: ./src/gromacs/utility/tests/mpicomm.cpp:160: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:168: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:181: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:194: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 18: [ RUN ] MpiComm.ConstructorThrowsOnNull 18: ./src/gromacs/utility/tests/mpicomm.cpp:206: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull (0 ms) 18: [ RUN ] MpiComm.CopyConstructorWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:220: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CopyConstructorWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:243: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:259: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:281: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:298: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 18: [----------] 12 tests from MpiComm (0 ms total) 18: 18: [----------] 1 test from PathTest 18: [ RUN ] PathTest.StripSourcePrefixWorks 18: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 18: [----------] 1 test from PathTest (0 ms total) 18: 18: [----------] 2 tests from PhysicalNodeCommunicatorTest 18: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 18: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 18: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 18: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 18: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 18: 18: [----------] 5 tests from Range 18: [ RUN ] Range.EmptyRangeWorks 18: [ OK ] Range.EmptyRangeWorks (0 ms) 18: [ RUN ] Range.NonEmptyRangeWorks 18: [ OK ] Range.NonEmptyRangeWorks (0 ms) 18: [ RUN ] Range.BeginEnd 18: [ OK ] Range.BeginEnd (0 ms) 18: [ RUN ] Range.IsInRangeWorks 18: [ OK ] Range.IsInRangeWorks (0 ms) 18: [ RUN ] Range.IteratorWorks 18: [ OK ] Range.IteratorWorks (0 ms) 18: [----------] 5 tests from Range (0 ms total) 18: 18: [----------] 3 tests from ScopeGuardTest 18: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 18: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 18: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 18: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 18: [----------] 3 tests from ScopeGuardTest (0 ms total) 18: 18: [----------] 7 tests from StringConvert 18: [ RUN ] StringConvert.NoResultFromEptyString 18: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 18: [ RUN ] StringConvert.ThreeFloatsSuccessfully 18: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 18: [ RUN ] StringConvert.OneIntSucessfully 18: [ OK ] StringConvert.OneIntSucessfully (0 ms) 18: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 18: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 18: [ RUN ] StringConvert.ThrowsWhenWrongSize 18: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 18: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 18: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 18: [----------] 7 tests from StringConvert (0 ms total) 18: 18: [----------] 7 tests from StringToEnumValueConverterTest 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 18: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 18: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 18: 18: [----------] 9 tests from StringUtilityTest 18: [ RUN ] StringUtilityTest.StartsWith 18: [ OK ] StringUtilityTest.StartsWith (0 ms) 18: [ RUN ] StringUtilityTest.EndsWith 18: [ OK ] StringUtilityTest.EndsWith (0 ms) 18: [ RUN ] StringUtilityTest.StripSuffixIfPresent 18: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 18: [ RUN ] StringUtilityTest.StripString 18: [ OK ] StringUtilityTest.StripString (0 ms) 18: [ RUN ] StringUtilityTest.SplitString 18: [ OK ] StringUtilityTest.SplitString (0 ms) 18: [ RUN ] StringUtilityTest.SplitDelimitedString 18: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 18: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 18: [----------] 9 tests from StringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from FormatStringTest 18: [ RUN ] FormatStringTest.HandlesBasicFormatting 18: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 18: [ RUN ] FormatStringTest.HandlesLongStrings 18: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 18: [----------] 2 tests from FormatStringTest (0 ms total) 18: 18: [----------] 1 test from StringFormatterTest 18: [ RUN ] StringFormatterTest.HandlesBasicFormatting 18: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 18: [----------] 1 test from StringFormatterTest (0 ms total) 18: 18: [----------] 1 test from formatAndJoinTest 18: [ RUN ] formatAndJoinTest.Works 18: [ OK ] formatAndJoinTest.Works (0 ms) 18: [----------] 1 test from formatAndJoinTest (0 ms total) 18: 18: [----------] 1 test from JoinStringsTest 18: [ RUN ] JoinStringsTest.Works 18: [ OK ] JoinStringsTest.Works (0 ms) 18: [----------] 1 test from JoinStringsTest (0 ms total) 18: 18: [----------] 6 tests from ReplaceAllTest 18: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 18: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesNoMatches 18: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 18: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 18: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 18: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 18: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 18: [----------] 6 tests from ReplaceAllTest (0 ms total) 18: 18: [----------] 10 tests from TextLineWrapperTest 18: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 18: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 18: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 18: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectly 18: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndent 18: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 18: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 18: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 18: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 18: [----------] 10 tests from TextLineWrapperTest (0 ms total) 18: 18: [----------] 1 test from PrettyPrintListAsRangeTest 18: [ RUN ] PrettyPrintListAsRangeTest.Works 18: [ OK ] PrettyPrintListAsRangeTest.Works (0 ms) 18: [----------] 1 test from PrettyPrintListAsRangeTest (0 ms total) 18: 18: [----------] 1 test from CompileTimeStringJoin 18: [ RUN ] CompileTimeStringJoin.Works 18: [ OK ] CompileTimeStringJoin.Works (0 ms) 18: [----------] 1 test from CompileTimeStringJoin (0 ms total) 18: 18: [----------] 3 tests from TemplateMPTest 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 18: [----------] 3 tests from TemplateMPTest (0 ms total) 18: 18: [----------] 8 tests from TextWriterTest 18: [ RUN ] TextWriterTest.WritesLines 18: [ OK ] TextWriterTest.WritesLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInParts 18: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 18: [ RUN ] TextWriterTest.WritesWrappedLines 18: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 18: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 18: [ RUN ] TextWriterTest.TracksNewlines 18: [ OK ] TextWriterTest.TracksNewlines (0 ms) 18: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 18: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 18: [ RUN ] TextWriterTest.WritesIndentedLines 18: [ OK ] TextWriterTest.WritesIndentedLines (0 ms) 18: [ RUN ] TextWriterTest.ScopedIndenterWritesIndentedLines 18: [ OK ] TextWriterTest.ScopedIndenterWritesIndentedLines (0 ms) 18: [----------] 8 tests from TextWriterTest (0 ms total) 18: 18: [----------] 4 tests from DumpingTextTest 18: [ RUN ] DumpingTextTest.LegacyIndentingWorks 18: [ OK ] DumpingTextTest.LegacyIndentingWorks (0 ms) 18: [ RUN ] DumpingTextTest.ReportsWhenNotAvailableIdentically 18: [ OK ] DumpingTextTest.ReportsWhenNotAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.QuietWhenAvailableIdentically 18: [ OK ] DumpingTextTest.QuietWhenAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.PrintsTitleAndSizeIdentically 18: [ OK ] DumpingTextTest.PrintsTitleAndSizeIdentically (0 ms) 18: [----------] 4 tests from DumpingTextTest (0 ms total) 18: 18: [----------] 1 test from TypeTraitsTest 18: [ RUN ] TypeTraitsTest.IsIntegralConstant 18: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 18: [----------] 1 test from TypeTraitsTest (0 ms total) 18: 18: [----------] 41 tests from RVecTest 18: [ RUN ] RVecTest.CanBeStoredInVector 18: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAsMutable_rvec 18: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Array 18: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 18: [ RUN ] RVecTest.ComparesEqual 18: [ OK ] RVecTest.ComparesEqual (0 ms) 18: [ RUN ] RVecTest.ComparesUnequal 18: [ OK ] RVecTest.ComparesUnequal (0 ms) 18: [ RUN ] RVecTest.CanAddRVecToRvec 18: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanAddAssignRVecToRvec 18: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractRVecFromRvec 18: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 18: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanDotProductRVecByRvec 18: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanCrossProductRVecByRvec 18: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVecInplace 18: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 18: [ RUN ] RVecTest.CanScaleRVec 18: [ OK ] RVecTest.CanScaleRVec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVec 18: [ OK ] RVecTest.CanDivideRVec (0 ms) 18: [ RUN ] RVecTest.CanDoUnitvFromRVec 18: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanSqLengthOfRVec 18: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanLengthOfRVec 18: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToRVec 18: [ OK ] RVecTest.CanCastToRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToDVec 18: [ OK ] RVecTest.CanCastToDVec (0 ms) 18: [ RUN ] RVecTest.CanLeftScalarMultiply 18: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanRightScalarMultiply 18: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanGetUnitvFromRVec 18: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanGetSqLengthOfRVec 18: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanGetLengthOfRVec 18: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoCrossProductOfRVec 18: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoDotProductOfRVec 18: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanScaleByVector 18: [ OK ] RVecTest.CanScaleByVector (0 ms) 18: [ RUN ] RVecTest.CanNegate 18: [ OK ] RVecTest.CanNegate (0 ms) 18: [ RUN ] RVecTest.asIVec 18: [ OK ] RVecTest.asIVec (0 ms) 18: [ RUN ] RVecTest.elementWiseMin 18: [ OK ] RVecTest.elementWiseMin (0 ms) 18: [ RUN ] RVecTest.elementWiseMax 18: [ OK ] RVecTest.elementWiseMax (0 ms) 18: [ RUN ] RVecTest.WorksAs_dvec_Reference 18: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_ivec_Reference 18: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Reference 18: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 18: [ RUN ] RVecTest.CopyConstructorWorks 18: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 18: [ RUN ] RVecTest.CopyAssignmentWorks 18: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.MoveConstructorWorks 18: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 18: [ RUN ] RVecTest.MoveAssignmentWorks 18: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.UsableInConstexpr 18: [ OK ] RVecTest.UsableInConstexpr (0 ms) 18: [----------] 41 tests from RVecTest (0 ms total) 18: 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 18: 18: [----------] 11 tests from WithInputPaths/PathSearchTest 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 18: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 18: 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 18: 18: [----------] 24 tests from Works/DumpingVectorsTest 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 (0 ms) 18: [----------] 24 tests from Works/DumpingVectorsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 495 tests from 68 test suites ran. (7 ms total) 18: [ PASSED ] 485 tests. 18: [ SKIPPED ] 10 tests, listed below: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull 18: [ SKIPPED ] MpiComm.CopyConstructorWorks 18: [ SKIPPED ] MpiComm.AssigmentWorks 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf 18: 18: YOU HAVE 1 DISABLED TEST 18: 18/104 Test #18: UtilityUnitTests .......................... Passed 0.02 sec test 19 Start 19: MpiCommTests 19: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mpicomm-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MpiCommTests.xml" 19: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests 19: Test timeout computed to be: 30 19: [==========] Running 12 tests from 1 test suite. 19: [----------] Global test environment set-up. 19: [----------] 12 tests from MpiComm 19: [ RUN ] MpiComm.SingleRankNoComm 19: [ OK ] MpiComm.SingleRankNoComm (0 ms) 19: [ RUN ] MpiComm.CommWorld 19: [ OK ] MpiComm.CommWorld (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 19: [ RUN ] MpiComm.ConstructorThrowsOnNull 19: [ OK ] MpiComm.ConstructorThrowsOnNull (0 ms) 19: [ RUN ] MpiComm.CopyConstructorWorks 19: [ OK ] MpiComm.CopyConstructorWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorks 19: [ OK ] MpiComm.AssigmentWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorksForSelf 19: [ OK ] MpiComm.AssigmentWorksForSelf (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorks 19: [ OK ] MpiComm.MoveAssigmentWorks (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 19: [ OK ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 19: [----------] 12 tests from MpiComm (2 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 12 tests from 1 test suite ran. (2 ms total) 19: [ PASSED ] 12 tests. 19/104 Test #19: MpiCommTests .............................. Passed 0.01 sec test 20 Start 20: UtilityMpiUnitTests 20: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/utility/tests 20: Test timeout computed to be: 30 20: [==========] Running 7 tests from 2 test suites. 20: [----------] Global test environment set-up. 20: [----------] 5 tests from CoordinateExceptionHandlingTest 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow (0 ms) 20: [----------] 5 tests from CoordinateExceptionHandlingTest (0 ms total) 20: 20: [----------] 2 tests from PhysicalNodeCommunicatorTest 20: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 20: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 20: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 20: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 20: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 7 tests from 2 test suites ran. (1 ms total) 20: [ PASSED ] 7 tests. 20/104 Test #20: UtilityMpiUnitTests ....................... Passed 0.01 sec test 21 Start 21: MdlibUnitTest 21: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdlibUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests 21: Test timeout computed to be: 30 21: [==========] Running 1042 tests from 29 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from EffectiveAtomDensity 21: [ RUN ] EffectiveAtomDensity.VolumeIndependence 21: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 21: [ RUN ] EffectiveAtomDensity.WeightingWorks 21: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 21: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 21: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 21: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 21: 21: [----------] 2 tests from AtomNonbondedAndKineticProperties 21: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 21: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 21: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 21: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 21: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 21: 21: [----------] 1 test from VerletBufferConstraintTest 21: [ RUN ] VerletBufferConstraintTest.EqualMasses 21: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 21: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 21: 21: [----------] 1 test from VerletBufferSize 21: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 21: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 21: [----------] 1 test from VerletBufferSize (0 ms total) 21: 21: [----------] 6 tests from CalcvirTest 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 21: [----------] 6 tests from CalcvirTest (2 ms total) 21: 21: [----------] 2 tests from PrEbinTest 21: [ RUN ] PrEbinTest.HandlesAverages 21: [ OK ] PrEbinTest.HandlesAverages (0 ms) 21: [ RUN ] PrEbinTest.HandlesEmptyAverages 21: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 21: [----------] 2 tests from PrEbinTest (0 ms total) 21: 21: [----------] 3 tests from EnergyDriftTracker 21: [ RUN ] EnergyDriftTracker.emptyWorks 21: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.onePointWorks 21: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.manyPointsWorks 21: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 21: [----------] 3 tests from EnergyDriftTracker (0 ms total) 21: 21: [----------] 4 tests from ShakeTest 21: [ RUN ] ShakeTest.ConstrainsOneBond 21: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 21: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 21: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 21: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 21: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 21: [----------] 4 tests from ShakeTest (0 ms total) 21: 21: [----------] 1 test from NullSignalTest 21: [ RUN ] NullSignalTest.NullSignallerWorks 21: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 21: [----------] 1 test from NullSignalTest (0 ms total) 21: 21: [----------] 7 tests from SignalTest 21: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 21: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 21: [----------] 7 tests from SignalTest (0 ms total) 21: 21: [----------] 13 tests from UpdateGroupsTest 21: [ RUN ] UpdateGroupsTest.WithEthaneUA 21: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 21: [ RUN ] UpdateGroupsTest.WithMethane 21: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithEthane 21: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 21: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 21: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFourSite 21: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 21: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 21: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 21: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 21: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 21: [----------] 13 tests from UpdateGroupsTest (0 ms total) 21: 21: [----------] 1 test from UpdateGroupsCog 21: [ RUN ] UpdateGroupsCog.ComputesCogs 21: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 21: [----------] 1 test from UpdateGroupsCog (0 ms total) 21: 21: [----------] 3 tests from VSiteTest 21: [ RUN ] VSiteTest.VSiteLowerConstructingWorks 21: [ OK ] VSiteTest.VSiteLowerConstructingWorks (0 ms) 21: [ RUN ] VSiteTest.VSiteHigherConstructingThrows 21: [ OK ] VSiteTest.VSiteHigherConstructingThrows (0 ms) 21: [ RUN ] VSiteTest.VSiteEqualConstructingThrows 21: [ OK ] VSiteTest.VSiteEqualConstructingThrows (0 ms) 21: [----------] 3 tests from VSiteTest (0 ms total) 21: 21: [----------] 2 tests from WholeMoleculeTransform 21: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 21: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 21: [ RUN ] WholeMoleculeTransform.HandlesReordering 21: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 21: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 21: 21: [----------] 28 tests from WithParameters/ConstraintsTest 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (4 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (3 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 21: [----------] 28 tests from WithParameters/ConstraintsTest (10 ms total) 21: 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 (1 ms) 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest (1 ms total) 21: 21: [----------] 11 tests from WithParameters/EnergyOutputTest 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 21: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 21: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 21: [----------] 11 tests from WithParameters/EnergyOutputTest (10 ms total) 21: 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 21: 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 21: 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 21: 21: [----------] 17 tests from WithParameters/LangevinTest 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 21: [----------] 17 tests from WithParameters/LangevinTest (1 ms total) 21: 21: [----------] 16 tests from WithParameters/LeapFrogTest 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 21: [----------] 16 tests from WithParameters/LeapFrogTest (9 ms total) 21: 21: [----------] 140 tests from Cubic/ParrRahmTest 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Cubic/ParrRahmTest (7 ms total) 21: 21: [----------] 140 tests from Rectilinear/ParrRahmTest 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Rectilinear/ParrRahmTest (7 ms total) 21: 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (7 ms total) 21: 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (8 ms total) 21: 21: [----------] 140 tests from TruncOct/ParrRahmTest 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from TruncOct/ParrRahmTest (9 ms total) 21: 21: [----------] 140 tests from Other/ParrRahmTest 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Other/ParrRahmTest (9 ms total) 21: 21: [----------] 13 tests from WithParameters/SettleTest 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 21: [----------] 13 tests from WithParameters/SettleTest (4 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1042 tests from 29 test suites ran. (94 ms total) 21: [ PASSED ] 1042 tests. 21/104 Test #21: MdlibUnitTest ............................. Passed 8.76 sec test 22 Start 22: AwhTest 22: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/AwhTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/awh/tests 22: Test timeout computed to be: 30 22: [==========] Running 27 tests from 10 test suites. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from SerializationTest 22: [ RUN ] SerializationTest.CanSerializeDimParams 22: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeBiasParams 22: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeAwhParams 22: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 22: [----------] 3 tests from SerializationTest (0 ms total) 22: 22: [----------] 1 test from BiasTest 22: [ RUN ] BiasTest.DetectsCovering 22: [ OK ] BiasTest.DetectsCovering (0 ms) 22: [----------] 1 test from BiasTest (0 ms total) 22: 22: [----------] 1 test from biasGridTest 22: [ RUN ] biasGridTest.neighborhood 22: [ OK ] biasGridTest.neighborhood (0 ms) 22: [----------] 1 test from biasGridTest (0 ms total) 22: 22: [----------] 2 tests from BiasSharingTest 22: [ RUN ] BiasSharingTest.SharingWorks 22: [ OK ] BiasSharingTest.SharingWorks (0 ms) 22: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 22: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (2 ms) 22: [----------] 2 tests from BiasSharingTest (3 ms total) 22: 22: [----------] 2 tests from BiasFepLambdaStateTest 22: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 22: [ OK ] BiasFepLambdaStateTest.DetectsCovering (2 ms) 22: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 22: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 22: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) 22: 22: [----------] 8 tests from WithParameters/BiasTest 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 22: [----------] 8 tests from WithParameters/BiasTest (2 ms total) 22: 22: [----------] 2 tests from WithParameters/BiasStateTest 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 22: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 22: 22: [----------] 1 test from WithParameters/UserInputTest 22: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 22: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 22: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 22: 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (15 ms total) 22: 22: [----------] 3 tests from WithParameters/FrictionMetricTest 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (10 ms) 22: [----------] 3 tests from WithParameters/FrictionMetricTest (12 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 27 tests from 10 test suites ran. (38 ms total) 22: [ PASSED ] 27 tests. 22/104 Test #22: AwhTest ................................... Passed 0.05 sec test 23 Start 23: DensityFittingAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/densityfitting/tests 23: Test timeout computed to be: 30 23: [==========] Running 18 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from DensityFittingTest 23: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 23: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 23: [ RUN ] DensityFittingTest.SingleAtom 23: [ OK ] DensityFittingTest.SingleAtom (0 ms) 23: [----------] 2 tests from DensityFittingTest (0 ms total) 23: 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest 23: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 23: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 23: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 23: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 23: 23: [----------] 1 test from DensityFittingForceProviderState 23: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 23: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 23: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 23: 23: [----------] 8 tests from DensityFittingOptionsTest 23: [ RUN ] DensityFittingOptionsTest.DefaultParameters 23: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 23: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 23: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 23: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 23: [ RUN ] DensityFittingOptionsTest.KvtToInternal 23: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 23: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 23: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 23: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 18 tests from 4 test suites ran. (1 ms total) 23: [ PASSED ] 18 tests. 23/104 Test #23: DensityFittingAppliedForcesUnitTest ....... Passed 0.01 sec test 24 Start 24: QMMMAppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests 24: Test timeout computed to be: 30 24: [==========] Running 28 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 2 tests from QMMMInputGeneratorTest 24: [ RUN ] QMMMInputGeneratorTest.CanConstruct 24: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 24: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 24: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 24: [----------] 2 tests from QMMMInputGeneratorTest (0 ms total) 24: 24: [----------] 6 tests from QMMMTopologyPreprocessorTest 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Setting the LD random seed to -17178699 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (3 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Setting the LD random seed to -185079818 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (3 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading -0.41000 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -37882115 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (3 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 63.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 129.093 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -268491269 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (7 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: 24: NOTE 2 [file unknown]: 24: You are using constraints on all bonds, whereas the forcefield has been 24: parametrized only with constraints involving hydrogen atoms. We suggest 24: using constraints = h-bonds instead, this will also improve performance. 24: 24: 24: NOTE 3 [file unknown]: 24: For energy conservation with LINCS, lincs_iter should be 2 or larger. 24: 24: 24: Number of degrees of freedom in T-Coupling group rest is 42.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 193.640 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 5 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: 24: WARNING 2 [file unknown]: 24: Your embedded subsystem has a lot of constrained bonds. They probably 24: have been generated automatically. That could produce artifacts in the 24: simulation. Consider constraints = none in the mdp file. 24: 24: 24: Setting the LD random seed to -41943169 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: turning all bonds into constraints... 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (8 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Number of degrees of freedom in T-Coupling group rest is 45.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 24: Setting the LD random seed to -537398305 24: 24: Generated 3 of the 6 non-bonded parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'VSTEST' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 24: 24: Cleaning up constraints and constant bonded interactions with virtual sites 24: Analysing residue names: 24: There are: 1 Other residues 24: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (3 ms) 24: [----------] 6 tests from QMMMTopologyPreprocessorTest (29 ms total) 24: 24: [----------] 9 tests from QMMMOptionsTest 24: [ RUN ] QMMMOptionsTest.DefaultParameters 24: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 24: [ RUN ] QMMMOptionsTest.OptionSetsActive 24: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 24: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 24: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 24: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 24: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 24: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 24: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 24: [----------] 9 tests from QMMMOptionsTest (0 ms total) 24: 24: [----------] 3 tests from QMMMForceProviderStateTest 24: [ RUN ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint 24: [ OK ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent 24: [ OK ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.MissingStateWhenNoData 24: [ OK ] QMMMForceProviderStateTest.MissingStateWhenNoData (0 ms) 24: [----------] 3 tests from QMMMForceProviderStateTest (0 ms total) 24: 24: [----------] 1 test from QMMMForceProviderTest 24: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 24: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 24: [----------] 1 test from QMMMForceProviderTest (0 ms total) 24: 24: [----------] 1 test from QMMMTest 24: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 24: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 24: [----------] 1 test from QMMMTest (0 ms total) 24: 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink (0 ms) 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 28 tests from 7 test suites ran. (31 ms total) 24: [ PASSED ] 28 tests. 24/104 Test #24: QMMMAppliedForcesUnitTest ................. Passed 0.04 sec test 25 Start 25: ColvarsAppliedForcesUnitTest 25: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests 25: Test timeout computed to be: 30 25: [==========] Running 16 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 1 test from ColvarsTest 25: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 25: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 25: [----------] 1 test from ColvarsTest (0 ms total) 25: 25: [----------] 6 tests from ColvarsOptionsTest 25: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 25: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OptionSetsActive 25: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to -16788826 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (4 ms) 25: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 25: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 25: [----------] 6 tests from ColvarsOptionsTest (5 ms total) 25: 25: [----------] 4 tests from ColvarsPreProcessorTest 25: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to 1912075358 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to -369164290 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to 1945590327 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (3 ms) 25: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to -70074390 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (2 ms) 25: [----------] 4 tests from ColvarsPreProcessorTest (12 ms total) 25: 25: [----------] 5 tests from ColvarsForceProviderTest 25: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 25: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 25: [ RUN ] ColvarsForceProviderTest.SimpleInputs 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to -541100408 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 25: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to 1232697327 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (2 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to -69210637 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForces4water (3 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 66.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: NVE simulation: will use the initial temperature of 300.368 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 25: Setting the LD random seed to -571089073 25: 25: Generated 2211 of the 2211 non-bonded parameter combinations 25: 25: Generated 2211 of the 2211 1-4 parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 25: Analysing residue names: 25: There are: 2 Protein residues 25: Analysing Protein... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (10 ms) 25: [----------] 5 tests from ColvarsForceProviderTest (20 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 16 tests from 4 test suites ran. (38 ms total) 25: [ PASSED ] 16 tests. 25/104 Test #25: ColvarsAppliedForcesUnitTest .............. Passed 0.05 sec test 26 Start 26: PlumedAppliedForcesUnitTests 26: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests 26: Test timeout computed to be: 30 26: [==========] Running 8 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 8 tests from PlumedOptionsTest 26: [ RUN ] PlumedOptionsTest.defaultConstructor 26: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 26: [ RUN ] PlumedOptionsTest.setTimeStep 26: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 26: [ RUN ] PlumedOptionsTest.setStartingBehavior 26: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFile 26: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 26: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 26: [ RUN ] PlumedOptionsTest.setTopology 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 21.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: 26: NOTE 2 [file angles1.top, line 72]: 26: In moleculetype 'butane' 4 atoms are not bound by a potential or 26: constraint to any other atom in the same moleculetype. Although 26: technically this might not cause issues in a simulation, this often means 26: that the user forgot to add a bond/potential/constraint or put multiple 26: molecules in the same moleculetype definition by mistake. Run with -v to 26: get information for each atom. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: NVE simulation: will use the initial temperature of 238.919 K for 26: determining the Verlet buffer size 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 17493.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: NVE simulation: will use the initial temperature of 67.983 K for 26: determining the Verlet buffer size 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 18.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: NVE simulation: will use the initial temperature of 135.187 K for 26: determining the Verlet buffer size 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 26: Setting the LD random seed to 1543501310 26: 26: Generated 10 of the 10 non-bonded parameter combinations 26: 26: Generated 10 of the 10 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Water residues 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -605028877 26: 26: Generated 3 of the 3 non-bonded parameter combinations 26: 26: Excluding 3 bonded neighbours molecule type 'butane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/angles1.gro' 26: Analysing residue names: 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -520767523 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Argon' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon5832.gro' 26: Analysing residue names: 26: There are: 5832 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -1610639876 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonA' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonB' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonC' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonD' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -1113669826 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Dipole' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 26: Analysing residue names: 26: There are: 2 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -209817610 26: 26: Generated 331705 of the 331705 non-bonded parameter combinations 26: 26: Generated 331705 of the 331705 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Excluding 3 bonded neighbours molecule type 'methane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 26: Analysing residue names: 26: There are: 1 Water residues 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: [ OK ] PlumedOptionsTest.setTopology (258 ms) 26: [----------] 8 tests from PlumedOptionsTest (259 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 8 tests from 1 test suite ran. (259 ms total) 26: [ PASSED ] 8 tests. 26/104 Test #26: PlumedAppliedForcesUnitTests .............. Passed 0.28 sec test 27 Start 27: PlumedMDTests 27: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/PlumedMDTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/plumed/tests 27: Test timeout computed to be: 600 27: [==========] Running 2 tests from 1 test suite. 27: [----------] Global test environment set-up. 27: [----------] 2 tests from SimplePlumedMD/PlumedRun 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 27: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 2 tests from 1 test suite ran. (14 ms total) 27: [ PASSED ] 0 tests. 27: [ SKIPPED ] 2 tests, listed below: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27/104 Test #27: PlumedMDTests ............................. Passed 0.03 sec test 28 Start 28: NNPotAppliedForcesUnitTest 28: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 28: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests 28: Test timeout computed to be: 30 28: [==========] Running 17 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 1 test from NNPotTest 28: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 28: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 28: [----------] 1 test from NNPotTest (0 ms total) 28: 28: [----------] 5 tests from NNPotOptionsTest 28: [ RUN ] NNPotOptionsTest.DefaultParameters 28: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 28: [ RUN ] NNPotOptionsTest.OptionSetsActive 28: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 28: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 28: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 28: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 28: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 28: [----------] 5 tests from NNPotOptionsTest (0 ms total) 28: 28: [----------] 1 test from NNPotForceProviderTest 28: [ RUN ] NNPotForceProviderTest.CanConstruct 28: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 28: [----------] 1 test from NNPotForceProviderTest (0 ms total) 28: 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Setting the LD random seed to -37822489 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 (4 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Setting the LD random seed to -824609859 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Setting the LD random seed to -445057027 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Setting the LD random seed to -74121697 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Setting the LD random seed to -134221161 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 (8 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: Setting the LD random seed to 2139094957 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 (8 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: 28: WARNING 1 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -65539 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 (8 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: 28: WARNING 2 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -311437891 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 (8 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Setting the LD random seed to -2695169 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 28: Setting the LD random seed to -2099384932 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 (3 ms) 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest (56 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 17 tests from 4 test suites ran. (57 ms total) 28: [ PASSED ] 17 tests. 28/104 Test #28: NNPotAppliedForcesUnitTest ................ Passed 0.08 sec test 29 Start 29: AppliedForcesUnitTest 29: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 29: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/applied_forces/tests 29: Test timeout computed to be: 30 29: [==========] Running 3 tests from 1 test suite. 29: [----------] Global test environment set-up. 29: [----------] 3 tests from ElectricFieldTest 29: [ RUN ] ElectricFieldTest.Static 29: [ OK ] ElectricFieldTest.Static (0 ms) 29: [ RUN ] ElectricFieldTest.Oscillating 29: [ OK ] ElectricFieldTest.Oscillating (0 ms) 29: [ RUN ] ElectricFieldTest.Pulsed 29: [ OK ] ElectricFieldTest.Pulsed (0 ms) 29: [----------] 3 tests from ElectricFieldTest (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 3 tests from 1 test suite ran. (0 ms total) 29: [ PASSED ] 3 tests. 29/104 Test #29: AppliedForcesUnitTest ..................... Passed 0.01 sec test 30 Start 30: ListedForcesTest 30: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/ListedForcesTest.xml" 30: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/listed_forces/tests 30: Test timeout computed to be: 30 30: [==========] Running 132 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from Bond/ListedForcesTest 30: [ RUN ] Bond/ListedForcesTest.Ifunc/0 30: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/1 30: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/2 30: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/3 30: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/4 30: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/5 30: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/6 30: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/7 30: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/8 30: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/9 30: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/10 30: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/11 30: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/12 30: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/13 30: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/14 30: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/15 30: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/16 30: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/17 30: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/18 30: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/19 30: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/20 30: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/21 30: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/22 30: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/23 30: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 30: [----------] 24 tests from Bond/ListedForcesTest (2 ms total) 30: 30: [----------] 33 tests from Angle/ListedForcesTest 30: [ RUN ] Angle/ListedForcesTest.Ifunc/0 30: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/1 30: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/2 30: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/3 30: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/4 30: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/5 30: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/6 30: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/7 30: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/8 30: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/9 30: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/10 30: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/11 30: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/12 30: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/13 30: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/14 30: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/15 30: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/16 30: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/17 30: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/18 30: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/19 30: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/20 30: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/21 30: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/22 30: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/23 30: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/24 30: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/25 30: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/26 30: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/27 30: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/28 30: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/29 30: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/30 30: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/31 30: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/32 30: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 30: [----------] 33 tests from Angle/ListedForcesTest (3 ms total) 30: 30: [----------] 18 tests from Dihedral/ListedForcesTest 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Dihedral/ListedForcesTest (2 ms total) 30: 30: [----------] 12 tests from Polarize/ListedForcesTest 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 30: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 30: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 30: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 30: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 30: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 30: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 30: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 30: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 30: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 30: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 30: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 30: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 30: 30: [----------] 18 tests from Restraints/ListedForcesTest 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 30: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 30: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 30: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 30: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 30: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 30: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 30: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 30: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 30: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 30: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 30: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 30: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 30: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 30: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 30: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 30: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 30: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 30: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Restraints/ListedForcesTest (2 ms total) 30: 30: [----------] 3 tests from BondZeroLength/ListedForcesTest 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 30: 30: [----------] 3 tests from AngleZero/ListedForcesTest 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 30: 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) 30: 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 132 tests from 9 test suites ran. (14 ms total) 30: [ PASSED ] 132 tests. 30/104 Test #30: ListedForcesTest .......................... Passed 0.03 sec test 31 Start 31: NbnxmTests 31: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nbnxm-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbnxmTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests 31: Test timeout computed to be: 30 31: [==========] Running 532 tests from 5 test suites. 31: [----------] Global test environment set-up. 31: [----------] 19 tests from KernelSetupTest 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 31: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 31: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeNone 31: [ OK ] KernelSetupTest.getCoulombKernelTypeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 31: [----------] 19 tests from KernelSetupTest (0 ms total) 31: 31: [----------] 2 tests from SimdEnergyAccumulatorTest 31: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 31: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 31: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 31: 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 31: 31: [----------] 504 tests from Combinations/NbnxmKernelTest 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [----------] 504 tests from Combinations/NbnxmKernelTest (426 ms total) 31: 31: [----------] 4 tests from WithParameters/PlainPairlistTest 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:241: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 (0 ms) 31: [----------] 4 tests from WithParameters/PlainPairlistTest (2 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 532 tests from 5 test suites ran. (429 ms total) 31: [ PASSED ] 189 tests. 31: [ SKIPPED ] 343 tests, listed below: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31/104 Test #31: NbnxmTests ................................ Passed 0.45 sec test 32 Start 32: NbnxmGpuTests 32: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/NbnxmGpuTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests 32: Test timeout computed to be: 30 32: This test program does NOT link in any test case. Please make sure this is intended. 32: [==========] Running 0 tests from 0 test suites. 32: [==========] 0 tests from 0 test suites ran. (0 ms total) 32: [ PASSED ] 0 tests. 32/104 Test #32: NbnxmGpuTests ............................. Passed 0.03 sec test 33 Start 33: GmxlibTests 33: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GmxlibTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests 33: Test timeout computed to be: 30 33: [==========] Running 78 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 72 tests from NBInteraction/NonbondedFepTest 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 33: [----------] 72 tests from NBInteraction/NonbondedFepTest (6 ms total) 33: 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 78 tests from 2 test suites ran. (7 ms total) 33: [ PASSED ] 78 tests. 33/104 Test #33: GmxlibTests ............................... Passed 0.02 sec test 34 Start 34: GmxlibGpuTests 34: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/nonbonded-fep-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GmxlibGpuTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/nbnxm/tests 34: Test timeout computed to be: 30 34: This test program does NOT link in any test case. Please make sure this is intended. 34: [==========] Running 0 tests from 0 test suites. 34: [==========] 0 tests from 0 test suites ran. (0 ms total) 34: [ PASSED ] 0 tests. 34/104 Test #34: GmxlibGpuTests ............................ Passed 0.02 sec test 35 Start 35: CommandLineUnitTests 35: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests 35: Test timeout computed to be: 30 35: [==========] Running 60 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from CommandLineHelpModuleTest 35: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 35: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 35: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 35: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 35: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 35: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 35: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 35: 35: [----------] 7 tests from CommandLineHelpWriterTest 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 35: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 35: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 35: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 35: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 35: 35: [----------] 6 tests from CommandLineModuleManagerTest 35: [ RUN ] CommandLineModuleManagerTest.RunsModule 35: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 35: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 35: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 35: 35: [----------] 13 tests from CommandLineParserTest 35: [ RUN ] CommandLineParserTest.HandlesSingleValues 35: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 35: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 35: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesString 35: [ OK ] CommandLineParserTest.HandlesString (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 35: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 35: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 35: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 35: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 35: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 35: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 35: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 35: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 35: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 35: [----------] 13 tests from CommandLineParserTest (0 ms total) 35: 35: [----------] 6 tests from CommandLineProgramContextTest 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 35: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 35: 35: [----------] 3 tests from OutputNamesTest 35: [ RUN ] OutputNamesTest.CanBeSuffixed 35: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 35: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 35: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 35: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 35: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 35: [----------] 3 tests from OutputNamesTest (0 ms total) 35: 35: [----------] 22 tests from ParseCommonArgsTest 35: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 35: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 35: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 35: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 35: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 35: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 35: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 35: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 35: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 35: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 35: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 35: Value is /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 35: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms) 35: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 35: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 35: [----------] 22 tests from ParseCommonArgsTest (4 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 60 tests from 7 test suites ran. (7 ms total) 35: [ PASSED ] 60 tests. 35/104 Test #35: CommandLineUnitTests ...................... Passed 0.02 sec test 36 Start 36: DomDecTests 36: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/DomDecTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests 36: Test timeout computed to be: 30 36: [==========] Running 9 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 7 tests from HashedMap 36: [ RUN ] HashedMap.InsertsFinds 36: [ OK ] HashedMap.InsertsFinds (0 ms) 36: [ RUN ] HashedMap.NegativeKeysWork 36: [ OK ] HashedMap.NegativeKeysWork (0 ms) 36: [ RUN ] HashedMap.InsertsErases 36: [ OK ] HashedMap.InsertsErases (0 ms) 36: [ RUN ] HashedMap.InsertsOrAssigns 36: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 36: [ RUN ] HashedMap.Clears 36: [ OK ] HashedMap.Clears (0 ms) 36: [ RUN ] HashedMap.LinkedEntries 36: [ OK ] HashedMap.LinkedEntries (0 ms) 36: [ RUN ] HashedMap.ResizesTable 36: [ OK ] HashedMap.ResizesTable (0 ms) 36: [----------] 7 tests from HashedMap (0 ms total) 36: 36: [----------] 2 tests from LocalAtomSetManager 36: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 36: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 36: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 36: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 36: [----------] 2 tests from LocalAtomSetManager (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 9 tests from 2 test suites ran. (0 ms total) 36: [ PASSED ] 9 tests. 36/104 Test #36: DomDecTests ............................... Passed 0.01 sec test 37 Start 37: DomDecMpiTests 37: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/DomDecMpiTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/domdec/tests 37: Test timeout computed to be: 30 37: [==========] Running 8 tests from 1 test suite. 37: [----------] Global test environment set-up. 37: [----------] 8 tests from Works/HaloExchangeTest 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/0 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/0 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/1 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/1 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/2 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/2 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/3 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/3 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/3 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 (0 ms) 37: [----------] 8 tests from Works/HaloExchangeTest (2 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 8 tests from 1 test suite ran. (2 ms total) 37: [ PASSED ] 4 tests. 37: [ SKIPPED ] 4 tests, listed below: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 37/104 Test #37: DomDecMpiTests ............................ Passed 0.03 sec test 38 Start 38: EwaldUnitTests 38: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/EwaldUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/ewald/tests 38: Test timeout computed to be: 30 38: [==========] Running 407 tests from 9 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from SeparatePmeRanksPermittedTest 38: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 38: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 38: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 38: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 38: 38: [----------] 108 tests from Pme_SplineAndSpreadTest 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [----------] 108 tests from Pme_SplineAndSpreadTest (91 ms total) 38: 38: [----------] 64 tests from Pme_SolveTest 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from Pme_SolveTest (11 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (3 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (5 ms total) 38: 38: [----------] 64 tests from PmeDiffEps_SolveTest 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from PmeDiffEps_SolveTest (10 ms total) 38: 38: [----------] 72 tests from Pme_GatherTest 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [----------] 72 tests from Pme_GatherTest (13 ms total) 38: 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 38: 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (3 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (29 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 407 tests from 9 test suites ran. (168 ms total) 38: [ PASSED ] 311 tests. 38: [ SKIPPED ] 96 tests, listed below: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38/104 Test #38: EwaldUnitTests ............................ Passed 0.20 sec test 39 Start 39: FFTUnitTests 39: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/FFTUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fft/tests 39: Test timeout computed to be: 1920 39: [==========] Running 15 tests from 4 test suites. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from ManyFFTTest 39: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (4 ms) 39: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (12 ms) 39: [----------] 2 tests from ManyFFTTest (17 ms total) 39: 39: [----------] 1 test from FFTTest 39: [ RUN ] FFTTest.Real2DLength18_15Test 39: [ OK ] FFTTest.Real2DLength18_15Test (3 ms) 39: [----------] 1 test from FFTTest (3 ms total) 39: 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (7 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (9 ms) 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (24 ms total) 39: 39: [----------] 2 tests from Works/ParameterizedFFTTest3D 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 39: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 15 tests from 4 test suites ran. (47 ms total) 39: [ PASSED ] 15 tests. 39/104 Test #39: FFTUnitTests .............................. Passed 0.07 sec test 40 Start 40: FmmInterfaceUnitTests 40: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/fmm-interface-tests "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/FmmInterfaceUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fmm/tests 40: Test timeout computed to be: 30 40: [==========] Running 18 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 10 tests from FmmMdpOptionsTest 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues 40: [ OK ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive 40: [ OK ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive (0 ms) 40: [----------] 10 tests from FmmMdpOptionsTest (0 ms total) 40: 40: [----------] 4 tests from FmmMdpValidatorTest 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings 40: 40: ERROR 1 [file unknown]: 40: ExaFMM expansion order must be greater than 0. 40: 40: 40: ERROR 1 [file unknown]: 40: ExaFMM direct range must be 2 when using GROMACS as a direct provider. 40: 40: 40: ERROR 1 [file unknown]: 40: Adaptive tree cannot be used for FMM when GROMACS is the direct provider. 40: Use a uniform tree instead. 40: 40: 40: ERROR 1 [file unknown]: 40: Maximum particles per cell for FMM must be set to a positive value when 40: using an adaptive tree. 40: 40: 40: ERROR 1 [file unknown]: 40: Tree depth for FMM is determined based on the domain decomposition grid 40: when using GROMACS as the direct provider and should not be set by the 40: user. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings 40: 40: ERROR 1 [file unknown]: 40: FMSolvr tree depth must be greater than or equal to 0. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings 40: [ OK ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm 40: 40: ERROR 1 [file unknown]: 40: FMM requires Coulomb interaction type to be FMM, but got PME 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm (0 ms) 40: [----------] 4 tests from FmmMdpValidatorTest (0 ms total) 40: 40: [----------] 1 test from FmmForceProviderTest 40: [ RUN ] FmmForceProviderTest.ThrowsWhenConstructingStub 40: [ OK ] FmmForceProviderTest.ThrowsWhenConstructingStub (0 ms) 40: [----------] 1 test from FmmForceProviderTest (0 ms total) 40: 40: [----------] 3 tests from FmmForceProviderBuilderTest 40: [ RUN ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady 40: [ OK ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup 40: [ OK ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider 40: [ OK ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider (0 ms) 40: [----------] 3 tests from FmmForceProviderBuilderTest (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 18 tests from 4 test suites ran. (1 ms total) 40: [ PASSED ] 18 tests. 40/104 Test #40: FmmInterfaceUnitTests ..................... Passed 0.01 sec test 41 Start 41: GpuUtilsUnitTests 41: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests 41: Test timeout computed to be: 30 41: [==========] Running 67 tests from 22 test suites. 41: [----------] Global test environment set-up. 41: [----------] 2 tests from ClfftInitializer 41: [ RUN ] ClfftInitializer.SingleInitializationWorks 41: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 41: [ RUN ] ClfftInitializer.TwoInitializationsWork 41: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 41: [----------] 2 tests from ClfftInitializer (0 ms total) 41: 41: [----------] 1 test from DevicesAvailable 41: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 41: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 41: [----------] 1 test from DevicesAvailable (0 ms total) 41: 41: [----------] 1 test from DeviceStreamManagerTest 41: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 41: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 41: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 41: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 41: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 41: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 41: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Swap 41: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Comparison 41: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 41: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 41: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Swap 41: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Comparison 41: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 41: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Swap 41: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Comparison 41: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 41: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Swap 41: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Comparison 41: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 41: 41: [----------] 1 test from HostAllocatorUntypedTest 41: [ RUN ] HostAllocatorUntypedTest.Comparison 41: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 41: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.Move 41: [ OK ] AllocatorTest/0.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/0 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.Move 41: [ OK ] AllocatorTest/1.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/1 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator,gmx::HostAllocationPolicy> 41: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.Move 41: [ OK ] AllocatorTest/2.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/2 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.Move 41: [ OK ] AllocatorTest/3.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/3 (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 67 tests from 22 test suites ran. (0 ms total) 41: [ PASSED ] 67 tests. 41/104 Test #41: GpuUtilsUnitTests ......................... Passed 0.03 sec test 42 Start 42: GpuUtilsMpiTests 42: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/gpu_utils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GpuUtilsMpiTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gpu_utils/tests 42: Test timeout computed to be: 30 42: [==========] Running 15 tests from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message (0 ms) 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/0_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/1_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/12000_values_in_message 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message (0 ms) 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest (2 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 15 tests from 1 test suite ran. (3 ms total) 42: [ PASSED ] 0 tests. 42: [ SKIPPED ] 15 tests, listed below: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: 42: YOU HAVE 3 DISABLED TESTS 42: 42/104 Test #42: GpuUtilsMpiTests .......................... Passed 0.03 sec test 43 Start 43: HardwareUnitTests 43: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/HardwareUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/hardware/tests 43: Test timeout computed to be: 30 43: [==========] Running 22 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 1 test from CpuInfoTest 43: [ RUN ] CpuInfoTest.SupportLevel 43: [ OK ] CpuInfoTest.SupportLevel (0 ms) 43: [----------] 1 test from CpuInfoTest (0 ms total) 43: 43: [----------] 4 tests from HardwareTopologyTest 43: [ RUN ] HardwareTopologyTest.Execute 43: [ OK ] HardwareTopologyTest.Execute (13 ms) 43: [ RUN ] HardwareTopologyTest.HwlocExecute 43: [ OK ] HardwareTopologyTest.HwlocExecute (11 ms) 43: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 43: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (10 ms) 43: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 43: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (10 ms) 43: [----------] 4 tests from HardwareTopologyTest (45 ms total) 43: 43: [----------] 1 test from DevicesManagerTest 43: [ RUN ] DevicesManagerTest.Serialization 43: [ OK ] DevicesManagerTest.Serialization (0 ms) 43: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 43: [----------] 1 test from DevicesManagerTest (0 ms total) 43: 43: [----------] 1 test from UuidStringTest 43: [ RUN ] UuidStringTest.Works 43: [ OK ] UuidStringTest.Works (0 ms) 43: [----------] 1 test from UuidStringTest (0 ms total) 43: 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (3 ms total) 43: 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) 43: 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 43: 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (1 ms total) 43: 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 43: 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 43: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (3 ms) 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (3 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 22 tests from 10 test suites ran. (59 ms total) 43: [ PASSED ] 22 tests. 43: 43: YOU HAVE 1 DISABLED TEST 43: 43/104 Test #43: HardwareUnitTests ......................... Passed 0.07 sec test 44 Start 44: MathUnitTests 44: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MathUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/math/tests 44: Test timeout computed to be: 30 44: [==========] Running 293 tests from 40 test suites. 44: [----------] Global test environment set-up. 44: [----------] 1 test from EmptyArrayRefWithPaddingTest 44: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 44: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 44: 44: [----------] 2 tests from InvertBoxMatrixTest 44: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 44: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 44: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 44: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 44: 44: [----------] 8 tests from ComplexNumberTest 44: [ RUN ] ComplexNumberTest.RealComplexMultiply 44: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 44: [ RUN ] ComplexNumberTest.RealComplexExp 44: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAdd 44: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexSubtract 44: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexMultiply 44: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexDivision 44: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexConjugate 44: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAbs2 44: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 44: [----------] 8 tests from ComplexNumberTest (0 ms total) 44: 44: [----------] 11 tests from TranslateAndScaleTest 44: [ RUN ] TranslateAndScaleTest.identityTransformation 44: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 44: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 44: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingIdentity 44: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 44: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 44: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 44: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 44: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 44: 44: [----------] 3 tests from AffineTransformationTest 44: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 44: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 44: [ RUN ] AffineTransformationTest.applyTransformationToVectors 44: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 44: [ RUN ] AffineTransformationTest.retrieveGradient 44: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 44: [----------] 3 tests from AffineTransformationTest (0 ms total) 44: 44: [----------] 14 tests from DensitySimilarityTest 44: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 44: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (17 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (16 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationCorrect 44: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 44: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 44: [----------] 14 tests from DensitySimilarityTest (35 ms total) 44: 44: [----------] 6 tests from StructureSimilarityTest 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 44: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 44: [----------] 6 tests from StructureSimilarityTest (0 ms total) 44: 44: [----------] 8 tests from ExponentialMovingAverage 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 44: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 44: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 44: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 44: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 44: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 44: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 44: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 44: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 44: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 44: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 44: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 44: 44: [----------] 21 tests from FunctionTest 44: [ RUN ] FunctionTest.StaticLog2 44: [ OK ] FunctionTest.StaticLog2 (0 ms) 44: [ RUN ] FunctionTest.Log2I32Bit 44: [ OK ] FunctionTest.Log2I32Bit (0 ms) 44: [ RUN ] FunctionTest.Log2I64Bit 44: [ OK ] FunctionTest.Log2I64Bit (0 ms) 44: [ RUN ] FunctionTest.GreatestCommonDivisor 44: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 44: [ RUN ] FunctionTest.InvsqrtFloat 44: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvsqrtDouble 44: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvsqrtInteger 44: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 44: [ RUN ] FunctionTest.InvcbrtFloat 44: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvcbrtDouble 44: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvcbrtInteger 44: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 44: [ RUN ] FunctionTest.SixthrootFloat 44: [ OK ] FunctionTest.SixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.SixthrootDouble 44: [ OK ] FunctionTest.SixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.SixthrootInteger 44: [ OK ] FunctionTest.SixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootFloat 44: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootDouble 44: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootInteger 44: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.Powers 44: [ OK ] FunctionTest.Powers (0 ms) 44: [ RUN ] FunctionTest.ErfInvFloat 44: [ OK ] FunctionTest.ErfInvFloat (0 ms) 44: [ RUN ] FunctionTest.ErfInvDouble 44: [ OK ] FunctionTest.ErfInvDouble (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 44: [----------] 21 tests from FunctionTest (1 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 44: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 44: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 44: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 44: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 44: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 44: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 44: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 44: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 44: 44: [----------] 4 tests from GaussianOn1DLattice 44: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 44: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 44: [ RUN ] GaussianOn1DLattice.isCorrect 44: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 44: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 44: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 44: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 44: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 44: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 44: 44: [----------] 9 tests from GaussTransformTest 44: [ RUN ] GaussTransformTest.isZeroUponConstruction 44: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 44: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 44: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 44: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 44: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 44: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 44: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 44: [ RUN ] GaussTransformTest.view 44: [ OK ] GaussTransformTest.view (0 ms) 44: [----------] 9 tests from GaussTransformTest (0 ms total) 44: 44: [----------] 3 tests from DensityFittingForce 44: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 44: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 44: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 44: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 44: [ RUN ] DensityFittingForce.pullsTowardsDerivative 44: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 44: [----------] 3 tests from DensityFittingForce (0 ms total) 44: 44: [----------] 2 tests from InvertMatrixTest 44: [ RUN ] InvertMatrixTest.IdentityIsImpotent 44: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertMatrixTest.ComputesInverse 44: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 44: [----------] 2 tests from InvertMatrixTest (0 ms total) 44: 44: [----------] 28 tests from MatrixTest 44: [ RUN ] MatrixTest.canSetFromArray 44: [ OK ] MatrixTest.canSetFromArray (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallyFromList 44: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallySingleValue 44: [ OK ] MatrixTest.canSetStaticallySingleValue (0 ms) 44: [ RUN ] MatrixTest.canConstructAndFill 44: [ OK ] MatrixTest.canConstructAndFill (0 ms) 44: [ RUN ] MatrixTest.canSetValues 44: [ OK ] MatrixTest.canSetValues (0 ms) 44: [ RUN ] MatrixTest.canCopyAssign 44: [ OK ] MatrixTest.canCopyAssign (0 ms) 44: [ RUN ] MatrixTest.canSwap 44: [ OK ] MatrixTest.canSwap (0 ms) 44: [ RUN ] MatrixTest.staticMultiDimArrayExtent 44: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MatrixTest.canAddMatrix 44: [ OK ] MatrixTest.canAddMatrix (0 ms) 44: [ RUN ] MatrixTest.canAddAssignMatrix 44: [ OK ] MatrixTest.canAddAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractMatrix 44: [ OK ] MatrixTest.canSubtractMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractAssignMatrix 44: [ OK ] MatrixTest.canSubtractAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canNegateMatrix 44: [ OK ] MatrixTest.canNegateMatrix (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarMultiplication 44: [ OK ] MatrixTest.MatrixScalarMultiplication (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarDivision 44: [ OK ] MatrixTest.MatrixScalarDivision (0 ms) 44: [ RUN ] MatrixTest.MatrixVectorMultiplicationOperator 44: [ OK ] MatrixTest.MatrixVectorMultiplicationOperator (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 44: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixMultiplication 44: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 44: [ RUN ] MatrixTest.determinantWorks 44: [ OK ] MatrixTest.determinantWorks (0 ms) 44: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 44: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 44: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 44: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 44: [ RUN ] MatrixTest.traceWorks 44: [ OK ] MatrixTest.traceWorks (0 ms) 44: [ RUN ] MatrixTest.transposeWorks 44: [ OK ] MatrixTest.transposeWorks (0 ms) 44: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 44: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 44: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 44: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.canFillLegacyMatrix 44: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.IdentityMatrix 44: [ OK ] MatrixTest.IdentityMatrix (0 ms) 44: [ RUN ] MatrixTest.DiagonalMatrix 44: [ OK ] MatrixTest.DiagonalMatrix (0 ms) 44: [----------] 28 tests from MatrixTest (0 ms total) 44: 44: [----------] 25 tests from MultiDimArrayTest 44: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 44: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 44: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 44: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 44: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 44: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 44: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 44: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 44: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 44: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 44: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 44: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 44: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapStatic 44: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapDynamic 44: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToView 44: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToConstView 44: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 44: [ RUN ] MultiDimArrayTest.viewBegin 44: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.viewEnd 44: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstBegin 44: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstEnd 44: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 44: [----------] 25 tests from MultiDimArrayTest (0 ms total) 44: 44: [----------] 4 tests from MultiDimArrayToMdSpanTest 44: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 44: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 44: 44: [----------] 9 tests from NelderMeadSimplexTest 44: [ RUN ] NelderMeadSimplexTest.BestVertex 44: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.WorstVertex 44: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 44: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 44: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 44: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 44: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 44: [ RUN ] NelderMeadSimplexTest.OrientedLength 44: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 44: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 44: 44: [----------] 2 tests from NelderMead 44: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 44: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 44: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 44: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 44: [----------] 2 tests from NelderMead (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ResizeWorks 44: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorks 44: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanCopyAssign 44: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanMoveAssign 44: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanSwap 44: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ResizeWorks 44: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorks 44: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanCopyAssign 44: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanMoveAssign 44: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanSwap 44: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ResizeWorks 44: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorks 44: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanCopyAssign 44: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanMoveAssign 44: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanSwap 44: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ResizeWorks 44: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorks 44: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanCopyAssign 44: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanMoveAssign 44: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanSwap 44: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ResizeWorks 44: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorks 44: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanCopyAssign 44: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanMoveAssign 44: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanSwap 44: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ResizeWorks 44: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorks 44: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanCopyAssign 44: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanMoveAssign 44: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanSwap 44: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ResizeWorks 44: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorks 44: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanCopyAssign 44: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanMoveAssign 44: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanSwap 44: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ResizeWorks 44: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorks 44: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanCopyAssign 44: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanMoveAssign 44: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanSwap 44: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ResizeWorks 44: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorks 44: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanCopyAssign 44: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanMoveAssign 44: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanSwap 44: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ResizeWorks 44: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorks 44: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanCopyAssign 44: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanMoveAssign 44: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanSwap 44: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 293 tests from 40 test suites ran. (40 ms total) 44: [ PASSED ] 293 tests. 44/104 Test #44: MathUnitTests ............................. Passed 0.06 sec test 45 Start 45: MdrunUtilityUnitTests 45: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests 45: Test timeout computed to be: 30 45: [==========] Running 33 tests from 3 test suites. 45: [----------] Global test environment set-up. 45: [----------] 4 tests from MDModulesNotifierTest 45: [ RUN ] MDModulesNotifierTest.AddConsumer 45: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 45: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 45: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 45: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 45: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 45: 45: [----------] 1 test from PlainPairlistRanges 45: [ RUN ] PlainPairlistRanges.RmsdDistance 45: [ OK ] PlainPairlistRanges.RmsdDistance (0 ms) 45: [----------] 1 test from PlainPairlistRanges (0 ms total) 45: 45: [----------] 28 tests from ThreadAffinityTest 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 45: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 45: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 45: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 45: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndFullMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndFullMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask (0 ms) 45: [ RUN ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall 45: [ OK ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithSmt (1 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToECoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem (0 ms) 45: [----------] 28 tests from ThreadAffinityTest (6 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 33 tests from 3 test suites ran. (6 ms total) 45: [ PASSED ] 33 tests. 45/104 Test #45: MdrunUtilityUnitTests ..................... Passed 0.02 sec test 46 Start 46: MdrunUtilityMpiUnitTests 46: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdrunutility/tests 46: Test timeout computed to be: 30 46: [==========] Running 17 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 10 tests from ThreadAffinityMultiRankTest 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 46: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (1 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (1 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 46: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 46: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp (5 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken (0 ms) 46: [----------] 10 tests from ThreadAffinityMultiRankTest (11 ms total) 46: 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (4 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 17 tests from 2 test suites ran. (16 ms total) 46: [ PASSED ] 17 tests. 46/104 Test #46: MdrunUtilityMpiUnitTests .................. Passed 0.03 sec test 47 Start 47: MDSpanTests 47: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MDSpanTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdspan/tests 47: Test timeout computed to be: 30 47: [==========] Running 32 tests from 7 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from BasicAccessorPolicy 47: [ RUN ] BasicAccessorPolicy.Decay 47: [ OK ] BasicAccessorPolicy.Decay (0 ms) 47: [ RUN ] BasicAccessorPolicy.Access 47: [ OK ] BasicAccessorPolicy.Access (0 ms) 47: [ RUN ] BasicAccessorPolicy.Offset 47: [ OK ] BasicAccessorPolicy.Offset (0 ms) 47: [ RUN ] BasicAccessorPolicy.CopyAccessor 47: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 47: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 47: 47: [----------] 4 tests from ExtentsTest 47: [ RUN ] ExtentsTest.Construction 47: [ OK ] ExtentsTest.Construction (0 ms) 47: [ RUN ] ExtentsTest.PurelyStatic 47: [ OK ] ExtentsTest.PurelyStatic (0 ms) 47: [ RUN ] ExtentsTest.RankNought 47: [ OK ] ExtentsTest.RankNought (0 ms) 47: [ RUN ] ExtentsTest.Assignment 47: [ OK ] ExtentsTest.Assignment (0 ms) 47: [----------] 4 tests from ExtentsTest (0 ms total) 47: 47: [----------] 8 tests from MdSpanExtension 47: [ RUN ] MdSpanExtension.SlicingAllStatic 47: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingDynamic 47: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingAllStatic3D 47: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 47: [ RUN ] MdSpanExtension.SlicingEqualsView3D 47: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 47: [ RUN ] MdSpanExtension.additionWorks 47: [ OK ] MdSpanExtension.additionWorks (0 ms) 47: [ RUN ] MdSpanExtension.subtractionWorks 47: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 47: [ RUN ] MdSpanExtension.multiplicationWorks 47: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 47: [ RUN ] MdSpanExtension.divisionWorks 47: [ OK ] MdSpanExtension.divisionWorks (0 ms) 47: [----------] 8 tests from MdSpanExtension (0 ms total) 47: 47: [----------] 3 tests from LayoutTests 47: [ RUN ] LayoutTests.LayoutRightConstruction 47: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 47: [ RUN ] LayoutTests.LayoutRightProperties 47: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 47: [ RUN ] LayoutTests.LayoutRightOperator 47: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 47: [----------] 3 tests from LayoutTests (0 ms total) 47: 47: [----------] 1 test from MdSpanTest 47: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 47: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 47: [----------] 1 test from MdSpanTest (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/0.Rank 47: [ OK ] MdSpanTest/0.Rank (0 ms) 47: [ RUN ] MdSpanTest/0.DynamicRank 47: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/0.Extents 47: [ OK ] MdSpanTest/0.Extents (0 ms) 47: [ RUN ] MdSpanTest/0.Strides 47: [ OK ] MdSpanTest/0.Strides (0 ms) 47: [ RUN ] MdSpanTest/0.Properties 47: [ OK ] MdSpanTest/0.Properties (0 ms) 47: [ RUN ] MdSpanTest/0.Operator 47: [ OK ] MdSpanTest/0.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/0 (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/1.Rank 47: [ OK ] MdSpanTest/1.Rank (0 ms) 47: [ RUN ] MdSpanTest/1.DynamicRank 47: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/1.Extents 47: [ OK ] MdSpanTest/1.Extents (0 ms) 47: [ RUN ] MdSpanTest/1.Strides 47: [ OK ] MdSpanTest/1.Strides (0 ms) 47: [ RUN ] MdSpanTest/1.Properties 47: [ OK ] MdSpanTest/1.Properties (0 ms) 47: [ RUN ] MdSpanTest/1.Operator 47: [ OK ] MdSpanTest/1.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/1 (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 32 tests from 7 test suites ran. (0 ms total) 47: [ PASSED ] 32 tests. 47/104 Test #47: MDSpanTests ............................... Passed 0.01 sec test 48 Start 48: MdtypesUnitTest 48: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/mdtypes/tests 48: Test timeout computed to be: 30 48: [==========] Running 98 tests from 7 test suites. 48: [----------] Global test environment set-up. 48: [----------] 4 tests from ForeingLambdaTermsDhdl 48: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 48: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 48: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 48: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 48: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 48: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 48: 48: [----------] 4 tests from ObservablesReducerTest 48: [ RUN ] ObservablesReducerTest.CanMoveAssign 48: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 48: [ RUN ] ObservablesReducerTest.CanMoveConstruct 48: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 48: [----------] 4 tests from ObservablesReducerTest (0 ms total) 48: 48: [----------] 3 tests from CheckpointDataTest 48: [ RUN ] CheckpointDataTest.SingleDataTest 48: [ OK ] CheckpointDataTest.SingleDataTest (2 ms) 48: [ RUN ] CheckpointDataTest.MultiDataTest 48: [ OK ] CheckpointDataTest.MultiDataTest (12 ms) 48: [ RUN ] CheckpointDataTest.EmptyVectorTest 48: [ OK ] CheckpointDataTest.EmptyVectorTest (0 ms) 48: [----------] 3 tests from CheckpointDataTest (15 ms total) 48: 48: [----------] 7 tests from ForceBuffers 48: [ RUN ] ForceBuffers.ConstructsUnpinned 48: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsPinned 48: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsEmpty 48: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 48: [ RUN ] ForceBuffers.ResizeWorks 48: [ OK ] ForceBuffers.ResizeWorks (0 ms) 48: [ RUN ] ForceBuffers.PaddingWorks 48: [ OK ] ForceBuffers.PaddingWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyWorks 48: [ OK ] ForceBuffers.CopyWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyDoesNotPin 48: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 48: [----------] 7 tests from ForceBuffers (0 ms total) 48: 48: [----------] 5 tests from MultipleTimeStepping 48: [ RUN ] MultipleTimeStepping.ChecksNumLevels 48: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 48: [ RUN ] MultipleTimeStepping.SelectsForceGroups 48: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksStepFactor 48: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 48: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksIntegrator 48: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 48: [----------] 5 tests from MultipleTimeStepping (0 ms total) 48: 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 48: 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 98 tests from 7 test suites ran. (16 ms total) 48: [ PASSED ] 98 tests. 48/104 Test #48: MdtypesUnitTest ........................... Passed 0.03 sec test 49 Start 49: OnlineHelpUnitTests 49: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/onlinehelp/tests 49: Test timeout computed to be: 30 49: [==========] Running 22 tests from 4 test suites. 49: [----------] Global test environment set-up. 49: [----------] 6 tests from TextTableFormatterTest 49: [ RUN ] TextTableFormatterTest.HandlesBasicCase 49: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesIndentation 49: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 49: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 49: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 49: [----------] 6 tests from TextTableFormatterTest (0 ms total) 49: 49: [----------] 3 tests from HelpManagerTest 49: [ RUN ] HelpManagerTest.HandlesRootTopic 49: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 49: [ RUN ] HelpManagerTest.HandlesSubTopics 49: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 49: [ RUN ] HelpManagerTest.HandlesInvalidTopics 49: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 49: [----------] 3 tests from HelpManagerTest (0 ms total) 49: 49: [----------] 2 tests from HelpTopicFormattingTest 49: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 49: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 49: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 49: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 49: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 49: 49: [----------] 11 tests from HelpWriterContextTest 49: [ RUN ] HelpWriterContextTest.FormatsParagraphs 49: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 49: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 49: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralText 49: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsBulletList 49: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 49: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 49: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsGridTable 49: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsTitles 49: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 49: [----------] 11 tests from HelpWriterContextTest (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 22 tests from 4 test suites ran. (1 ms total) 49: [ PASSED ] 22 tests. 49/104 Test #49: OnlineHelpUnitTests ....................... Passed 0.01 sec test 50 Start 50: OptionsUnitTests 50: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/OptionsUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/options/tests 50: Test timeout computed to be: 30 50: [==========] Running 151 tests from 21 test suites. 50: [----------] Global test environment set-up. 50: [----------] 5 tests from AbstractOptionStorageTest 50: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 50: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 50: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 50: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 50: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 50: 50: [----------] 10 tests from FileNameOptionTest 50: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 50: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 50: [----------] 10 tests from FileNameOptionTest (0 ms total) 50: 50: [----------] 16 tests from FileNameOptionManagerTest 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 50: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 50: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 50: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 50: 50: [----------] 1 test from OptionsTest 50: [ RUN ] OptionsTest.FailsOnNonsafeStorage 50: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 50: [----------] 1 test from OptionsTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerTest 50: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 50: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 50: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMissingValue 50: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesExtraValue 50: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesGroups 50: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesSections 50: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 50: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 50: [----------] 9 tests from OptionsAssignerTest (0 ms total) 50: 50: [----------] 4 tests from OptionsAssignerBooleanTest 50: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 50: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 50: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 50: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 50: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 50: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerIntegerTest 50: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerInt64Test 50: [ RUN ] OptionsAssignerInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresToVector 50: [ OK ] OptionsAssignerInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerInt64Test (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresToVector 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test (0 ms total) 50: 50: [----------] 5 tests from OptionsAssignerDoubleTest 50: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 50: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 50: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 50: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerStringTest 50: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 50: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 50: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 50: 50: [----------] 6 tests from OptionsAssignerEnumTest 50: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 50: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 50: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 50: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 50: 50: [----------] 8 tests from RepeatingOptionSectionTest 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 50: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 50: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 50: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 50: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 50: 50: [----------] 1 test from TimeUnitManagerTest 50: [ RUN ] TimeUnitManagerTest.BasicOperations 50: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 50: [----------] 1 test from TimeUnitManagerTest (0 ms total) 50: 50: [----------] 4 tests from TimeUnitBehaviorTest 50: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 50: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 50: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 50: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 50: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 50: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 50: 50: [----------] 2 tests from TreeValueSupportAssignTest 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 50: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 50: 50: [----------] 1 test from TreeValueSupportAssignErrorTest 50: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 50: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 50: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 50: 50: [----------] 5 tests from TreeValueSupportCheckTest 50: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 50: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 50: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 50: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 50: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 50: 50: [----------] 6 tests from TreeValueSupportAdjustTest 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 50: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 50: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 50: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 50: 50: [----------] 7 tests from TreeValueSupportTest 50: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 50: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 50: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsInt64Option 50: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsStringOption 50: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsFloatOption 50: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 50: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsEnumOption 50: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 50: [----------] 7 tests from TreeValueSupportTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 151 tests from 21 test suites ran. (3 ms total) 50: [ PASSED ] 151 tests. 50/104 Test #50: OptionsUnitTests .......................... Passed 0.01 sec test 51 Start 51: PbcutilUnitTest 51: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 51: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pbcutil/tests 51: Test timeout computed to be: 30 51: [==========] Running 37 tests from 5 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ShiftTest 51: [ RUN ] ShiftTest.CoordinateShiftWorks 51: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 51: [----------] 1 test from ShiftTest (0 ms total) 51: 51: [----------] 2 tests from MShift 51: [ RUN ] MShift.shiftsAndUnshifts 51: [ OK ] MShift.shiftsAndUnshifts (0 ms) 51: [ RUN ] MShift.shiftsAndUnshiftsSelf 51: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 51: [----------] 2 tests from MShift (0 ms total) 51: 51: [----------] 5 tests from PbcTest 51: [ RUN ] PbcTest.CalcShiftsWorks 51: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 51: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 51: [----------] 5 tests from PbcTest (0 ms total) 51: 51: [----------] 2 tests from PbcEnumsTest 51: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 51: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 51: [----------] 2 tests from PbcEnumsTest (0 ms total) 51: 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (3 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 37 tests from 5 test suites ran. (3 ms total) 51: [ PASSED ] 37 tests. 51/104 Test #51: PbcutilUnitTest ........................... Passed 0.01 sec test 52 Start 52: RandomUnitTests 52: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/RandomUnitTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/random/tests 52: Test timeout computed to be: 30 52: [==========] Running 44 tests from 10 test suites. 52: [----------] Global test environment set-up. 52: [----------] 4 tests from ExponentialDistributionTest 52: [ RUN ] ExponentialDistributionTest.Output 52: [ OK ] ExponentialDistributionTest.Output (0 ms) 52: [ RUN ] ExponentialDistributionTest.Logical 52: [ OK ] ExponentialDistributionTest.Logical (0 ms) 52: [ RUN ] ExponentialDistributionTest.Reset 52: [ OK ] ExponentialDistributionTest.Reset (0 ms) 52: [ RUN ] ExponentialDistributionTest.AltParam 52: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 52: 52: [----------] 4 tests from GammaDistributionTest 52: [ RUN ] GammaDistributionTest.Output 52: [ OK ] GammaDistributionTest.Output (0 ms) 52: [ RUN ] GammaDistributionTest.Logical 52: [ OK ] GammaDistributionTest.Logical (0 ms) 52: [ RUN ] GammaDistributionTest.Reset 52: [ OK ] GammaDistributionTest.Reset (0 ms) 52: [ RUN ] GammaDistributionTest.AltParam 52: [ OK ] GammaDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from GammaDistributionTest (0 ms total) 52: 52: [----------] 4 tests from NormalDistributionTest 52: [ RUN ] NormalDistributionTest.Output 52: [ OK ] NormalDistributionTest.Output (0 ms) 52: [ RUN ] NormalDistributionTest.Logical 52: [ OK ] NormalDistributionTest.Logical (0 ms) 52: [ RUN ] NormalDistributionTest.Reset 52: [ OK ] NormalDistributionTest.Reset (0 ms) 52: [ RUN ] NormalDistributionTest.AltParam 52: [ OK ] NormalDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from NormalDistributionTest (0 ms total) 52: 52: [----------] 1 test from SeedTest 52: [ RUN ] SeedTest.makeRandomSeed 52: [ OK ] SeedTest.makeRandomSeed (0 ms) 52: [----------] 1 test from SeedTest (0 ms total) 52: 52: [----------] 6 tests from TabulatedNormalDistributionTest 52: [ RUN ] TabulatedNormalDistributionTest.Output14 52: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Output16 52: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 52: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Logical 52: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Reset 52: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.AltParam 52: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 52: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 52: 52: [----------] 1 test from TabulatedNormalDistributionTableTest 52: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 52: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 52: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 52: 52: [----------] 6 tests from ThreeFry2x64Test 52: [ RUN ] ThreeFry2x64Test.Logical 52: [ OK ] ThreeFry2x64Test.Logical (0 ms) 52: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 52: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 52: [ RUN ] ThreeFry2x64Test.Reseed 52: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 52: [ RUN ] ThreeFry2x64Test.Discard 52: [ OK ] ThreeFry2x64Test.Discard (0 ms) 52: [ RUN ] ThreeFry2x64Test.InvalidCounter 52: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 52: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 52: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 52: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 52: 52: [----------] 4 tests from UniformIntDistributionTest 52: [ RUN ] UniformIntDistributionTest.Output 52: [ OK ] UniformIntDistributionTest.Output (0 ms) 52: [ RUN ] UniformIntDistributionTest.Logical 52: [ OK ] UniformIntDistributionTest.Logical (0 ms) 52: [ RUN ] UniformIntDistributionTest.Reset 52: [ OK ] UniformIntDistributionTest.Reset (0 ms) 52: [ RUN ] UniformIntDistributionTest.AltParam 52: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 52: 52: [----------] 5 tests from UniformRealDistributionTest 52: [ RUN ] UniformRealDistributionTest.GenerateCanonical 52: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Output 52: [ OK ] UniformRealDistributionTest.Output (0 ms) 52: [ RUN ] UniformRealDistributionTest.Logical 52: [ OK ] UniformRealDistributionTest.Logical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Reset 52: [ OK ] UniformRealDistributionTest.Reset (0 ms) 52: [ RUN ] UniformRealDistributionTest.AltParam 52: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 52: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 52: 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 44 tests from 10 test suites ran. (2 ms total) 52: [ PASSED ] 44 tests. 52/104 Test #52: RandomUnitTests ........................... Passed 0.01 sec test 53 Start 53: RestraintTests 53: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/RestraintTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/restraint/tests 53: Test timeout computed to be: 30 53: [==========] Running 1 test from 1 test suite. 53: [----------] Global test environment set-up. 53: [----------] 1 test from RestraintManager 53: [ RUN ] RestraintManager.restraintList 53: [ OK ] RestraintManager.restraintList (0 ms) 53: [----------] 1 test from RestraintManager (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 1 test from 1 test suite ran. (0 ms total) 53: [ PASSED ] 1 test. 53/104 Test #53: RestraintTests ............................ Passed 0.01 sec test 54 Start 54: SerializationUnitTests 54: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/serialization-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/SerializationUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/serialization/tests 54: Test timeout computed to be: 30 54: [==========] Running 9 tests from 2 test suites. 54: [----------] Global test environment set-up. 54: [----------] 5 tests from InMemorySerializerTest 54: [ RUN ] InMemorySerializerTest.Roundtrip 54: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 54: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 54: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SizeIsCorrect 54: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 54: [----------] 5 tests from InMemorySerializerTest (0 ms total) 54: 54: [----------] 4 tests from KeyValueTreeSerializerTest 54: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 54: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 54: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 54: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 9 tests from 2 test suites ran. (0 ms total) 54: [ PASSED ] 9 tests. 54/104 Test #54: SerializationUnitTests .................... Passed 0.01 sec test 55 Start 55: TableUnitTests 55: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/TableUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tables/tests 55: Test timeout computed to be: 30 55: [==========] Running 20 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 55: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/0.Sinc 55: [ OK ] SplineTableTest/0.Sinc (0 ms) 55: [ RUN ] SplineTableTest/0.LJ12 55: [ OK ] SplineTableTest/0.LJ12 (6 ms) 55: [ RUN ] SplineTableTest/0.PmeCorrection 55: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/0.TwoFunctions 55: [ OK ] SplineTableTest/0.TwoFunctions (10 ms) 55: [ RUN ] SplineTableTest/0.ThreeFunctions 55: [ OK ] SplineTableTest/0.ThreeFunctions (10 ms) 55: [ RUN ] SplineTableTest/0.Simd 55: [ OK ] SplineTableTest/0.Simd (2 ms) 55: [ RUN ] SplineTableTest/0.SimdTwoFunctions 55: [ OK ] SplineTableTest/0.SimdTwoFunctions (9 ms) 55: [----------] 10 tests from SplineTableTest/0 (40 ms total) 55: 55: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 55: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/1.Sinc 55: [ OK ] SplineTableTest/1.Sinc (0 ms) 55: [ RUN ] SplineTableTest/1.LJ12 55: [ OK ] SplineTableTest/1.LJ12 (0 ms) 55: [ RUN ] SplineTableTest/1.PmeCorrection 55: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/1.TwoFunctions 55: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 55: [ RUN ] SplineTableTest/1.ThreeFunctions 55: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 55: [ RUN ] SplineTableTest/1.Simd 55: [ OK ] SplineTableTest/1.Simd (0 ms) 55: [ RUN ] SplineTableTest/1.SimdTwoFunctions 55: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 55: [----------] 10 tests from SplineTableTest/1 (6 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 20 tests from 2 test suites ran. (47 ms total) 55: [ PASSED ] 20 tests. 55/104 Test #55: TableUnitTests ............................ Passed 0.06 sec test 56 Start 56: TaskAssignmentUnitTests 56: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/taskassignment/tests 56: Test timeout computed to be: 30 56: [==========] Running 3 tests from 2 test suites. 56: [----------] Global test environment set-up. 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 56: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 56: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 56: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 56: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 56: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 56: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 3 tests from 2 test suites ran. (0 ms total) 56: [ PASSED ] 3 tests. 56/104 Test #56: TaskAssignmentUnitTests ................... Passed 0.01 sec test 57 Start 57: GmxTimingTests 57: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GmxTimingTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/timing/tests 57: Test timeout computed to be: 30 57: [==========] Running 6 tests from 1 test suite. 57: [----------] Global test environment set-up. 57: [----------] 6 tests from TimingTest 57: [ RUN ] TimingTest.ElementCountingWorks 57: [ OK ] TimingTest.ElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.ElementNoCountingWorks 57: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementCountingWorks 57: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementNoCountingWorks 57: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.RunWallCycle 57: [ OK ] TimingTest.RunWallCycle (1 ms) 57: [ RUN ] TimingTest.RunWallCycleSub 57: [ OK ] TimingTest.RunWallCycleSub (0 ms) 57: [----------] 6 tests from TimingTest (1 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 6 tests from 1 test suite ran. (1 ms total) 57: [ PASSED ] 6 tests. 57/104 Test #57: GmxTimingTests ............................ Passed 0.01 sec test 58 Start 58: TopologyTest 58: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/TopologyTest.xml" 58: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/topology/tests 58: Test timeout computed to be: 30 58: [==========] Running 153 tests from 10 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from PdbAtomEntryTest 58: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 58: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 58: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 58: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 58: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 58: 58: [----------] 3 tests from ExclusionBlockTest 58: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 58: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 58: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 58: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 58: [ RUN ] ExclusionBlockTest.MergeExclusions 58: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 58: [----------] 3 tests from ExclusionBlockTest (0 ms total) 58: 58: [----------] 6 tests from InteractionListTest 58: [ RUN ] InteractionListTest.EmptyWorks 58: [ OK ] InteractionListTest.EmptyWorks (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArray 58: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 58: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionPointer 58: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 58: [ RUN ] InteractionListTest.CanAddListToOtherList 58: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 58: [ RUN ] InteractionListTest.ClearingWorks 58: [ OK ] InteractionListTest.ClearingWorks (0 ms) 58: [----------] 6 tests from InteractionListTest (0 ms total) 58: 58: [----------] 3 tests from IndexTest 58: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 58: [ RUN ] IndexTest.WriteIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteIndexWorks (1 ms) 58: [ RUN ] IndexTest.WriteAndReadIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 58: [----------] 3 tests from IndexTest (5 ms total) 58: 58: [----------] 4 tests from MtopTest 58: [ RUN ] MtopTest.RangeBasedLoop 58: [ OK ] MtopTest.RangeBasedLoop (0 ms) 58: [ RUN ] MtopTest.Operators 58: [ OK ] MtopTest.Operators (0 ms) 58: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 58: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 58: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 58: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 58: [----------] 4 tests from MtopTest (0 ms total) 58: 58: [----------] 2 tests from IListRangeTest 58: [ RUN ] IListRangeTest.RangeBasedLoopWorks 58: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 58: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 58: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 58: [----------] 2 tests from IListRangeTest (0 ms total) 58: 58: [----------] 13 tests from StringTableTest 58: [ RUN ] StringTableTest.AddSingleEntry 58: [ OK ] StringTableTest.AddSingleEntry (0 ms) 58: [ RUN ] StringTableTest.CanAccessWithAt 58: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 58: [ RUN ] StringTableTest.CanAccessWithBracket 58: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 58: [ RUN ] StringTableTest.ThrowsOutOfRange 58: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 58: [ RUN ] StringTableTest.StringCompareIsCorrect 58: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 58: [ RUN ] StringTableTest.AddTwoDistinctEntries 58: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] StringTableTest.TryToAddDuplicates 58: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 58: [ RUN ] StringTableTest.AddLargeNumberOfEntries 58: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 58: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 58: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 58: [ RUN ] StringTableTest.CanWriteToBuffer 58: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 58: [ RUN ] StringTableTest.Roundtrip 58: [ OK ] StringTableTest.Roundtrip (0 ms) 58: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 58: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 58: [ RUN ] StringTableTest.CanCopyToLegacyTable 58: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 58: [----------] 13 tests from StringTableTest (1 ms total) 58: 58: [----------] 6 tests from LegacySymtabTest 58: [ RUN ] LegacySymtabTest.EmptyOnOpen 58: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 58: [ RUN ] LegacySymtabTest.AddSingleEntry 58: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 58: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 58: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] LegacySymtabTest.TryToAddDuplicates 58: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 58: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 58: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 58: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 58: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 58: [----------] 6 tests from LegacySymtabTest (0 ms total) 58: 58: [----------] 5 tests from TopSortTest 58: [ RUN ] TopSortTest.WorksOnEmptyIdef 58: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 58: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 58: [----------] 5 tests from TopSortTest (0 ms total) 58: 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (7 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 153 tests from 10 test suites ran. (14 ms total) 58: [ PASSED ] 153 tests. 58: 58: YOU HAVE 1 DISABLED TEST 58: 58/104 Test #58: TopologyTest .............................. Passed 0.03 sec test 59 Start 59: PullTest 59: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/PullTest.xml" 59: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/pulling/tests 59: Test timeout computed to be: 30 59: [==========] Running 10 tests from 1 test suite. 59: [----------] Global test environment set-up. 59: [----------] 10 tests from PullTest 59: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 59: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 59: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 59: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 59: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 59: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 59: [ RUN ] PullTest.TransformationCoordSimple 59: [ OK ] PullTest.TransformationCoordSimple (0 ms) 59: [ RUN ] PullTest.TransformationCoordAdvanced 59: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 59: [ RUN ] PullTest.TransformationCoordTime 59: [ OK ] PullTest.TransformationCoordTime (0 ms) 59: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 59: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 59: [ RUN ] PullTest.TransformationCoordDummyExpression 59: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 59: [----------] 10 tests from PullTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 10 tests from 1 test suite ran. (0 ms total) 59: [ PASSED ] 10 tests. 59/104 Test #59: PullTest .................................. Passed 0.01 sec test 60 Start 60: SimdUnitTests 60: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/SimdUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/simd/tests 60: Test timeout computed to be: 30 60: [==========] Running 288 tests from 22 test suites. 60: [----------] Global test environment set-up. 60: [----------] 9 tests from SimdBootstrapTest 60: [ RUN ] SimdBootstrapTest.loadStore 60: [ OK ] SimdBootstrapTest.loadStore (0 ms) 60: [ RUN ] SimdBootstrapTest.loadU 60: [ OK ] SimdBootstrapTest.loadU (0 ms) 60: [ RUN ] SimdBootstrapTest.storeU 60: [ OK ] SimdBootstrapTest.storeU (0 ms) 60: [ RUN ] SimdBootstrapTest.loadStoreI 60: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 60: [ RUN ] SimdBootstrapTest.loadUI 60: [ OK ] SimdBootstrapTest.loadUI (0 ms) 60: [ RUN ] SimdBootstrapTest.storeUI 60: [ OK ] SimdBootstrapTest.storeUI (0 ms) 60: [ RUN ] SimdBootstrapTest.simd4LoadStore 60: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 60: [ RUN ] SimdBootstrapTest.simd4LoadU 60: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 60: [ RUN ] SimdBootstrapTest.simd4StoreU 60: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 60: [----------] 9 tests from SimdBootstrapTest (0 ms total) 60: 60: [----------] 41 tests from SimdScalarTest 60: [ RUN ] SimdScalarTest.load 60: [ OK ] SimdScalarTest.load (0 ms) 60: [ RUN ] SimdScalarTest.loadU 60: [ OK ] SimdScalarTest.loadU (0 ms) 60: [ RUN ] SimdScalarTest.store 60: [ OK ] SimdScalarTest.store (0 ms) 60: [ RUN ] SimdScalarTest.storeU 60: [ OK ] SimdScalarTest.storeU (0 ms) 60: [ RUN ] SimdScalarTest.setZero 60: [ OK ] SimdScalarTest.setZero (0 ms) 60: [ RUN ] SimdScalarTest.andNot 60: [ OK ] SimdScalarTest.andNot (0 ms) 60: [ RUN ] SimdScalarTest.fma 60: [ OK ] SimdScalarTest.fma (0 ms) 60: [ RUN ] SimdScalarTest.fms 60: [ OK ] SimdScalarTest.fms (0 ms) 60: [ RUN ] SimdScalarTest.fnma 60: [ OK ] SimdScalarTest.fnma (0 ms) 60: [ RUN ] SimdScalarTest.fnms 60: [ OK ] SimdScalarTest.fnms (0 ms) 60: [ RUN ] SimdScalarTest.maskAdd 60: [ OK ] SimdScalarTest.maskAdd (0 ms) 60: [ RUN ] SimdScalarTest.maskzMul 60: [ OK ] SimdScalarTest.maskzMul (0 ms) 60: [ RUN ] SimdScalarTest.maskzFma 60: [ OK ] SimdScalarTest.maskzFma (0 ms) 60: [ RUN ] SimdScalarTest.abs 60: [ OK ] SimdScalarTest.abs (0 ms) 60: [ RUN ] SimdScalarTest.max 60: [ OK ] SimdScalarTest.max (0 ms) 60: [ RUN ] SimdScalarTest.min 60: [ OK ] SimdScalarTest.min (0 ms) 60: [ RUN ] SimdScalarTest.round 60: [ OK ] SimdScalarTest.round (0 ms) 60: [ RUN ] SimdScalarTest.trunc 60: [ OK ] SimdScalarTest.trunc (0 ms) 60: [ RUN ] SimdScalarTest.reduce 60: [ OK ] SimdScalarTest.reduce (0 ms) 60: [ RUN ] SimdScalarTest.testBits 60: [ OK ] SimdScalarTest.testBits (0 ms) 60: [ RUN ] SimdScalarTest.anyTrue 60: [ OK ] SimdScalarTest.anyTrue (0 ms) 60: [ RUN ] SimdScalarTest.selectByMask 60: [ OK ] SimdScalarTest.selectByMask (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMask 60: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 60: [ RUN ] SimdScalarTest.blend 60: [ OK ] SimdScalarTest.blend (0 ms) 60: [ RUN ] SimdScalarTest.cvtR2I 60: [ OK ] SimdScalarTest.cvtR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvttR2I 60: [ OK ] SimdScalarTest.cvttR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvtI2R 60: [ OK ] SimdScalarTest.cvtI2R (0 ms) 60: [ RUN ] SimdScalarTest.cvtF2D 60: [ OK ] SimdScalarTest.cvtF2D (0 ms) 60: [ RUN ] SimdScalarTest.cvtD2D 60: [ OK ] SimdScalarTest.cvtD2D (0 ms) 60: [ RUN ] SimdScalarTest.loadI 60: [ OK ] SimdScalarTest.loadI (0 ms) 60: [ RUN ] SimdScalarTest.loadUI 60: [ OK ] SimdScalarTest.loadUI (0 ms) 60: [ RUN ] SimdScalarTest.storeI 60: [ OK ] SimdScalarTest.storeI (0 ms) 60: [ RUN ] SimdScalarTest.storeUI 60: [ OK ] SimdScalarTest.storeUI (0 ms) 60: [ RUN ] SimdScalarTest.andNotI 60: [ OK ] SimdScalarTest.andNotI (0 ms) 60: [ RUN ] SimdScalarTest.testBitsI 60: [ OK ] SimdScalarTest.testBitsI (0 ms) 60: [ RUN ] SimdScalarTest.selectByMaskI 60: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMaskI 60: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 60: [ RUN ] SimdScalarTest.blendI 60: [ OK ] SimdScalarTest.blendI (0 ms) 60: [ RUN ] SimdScalarTest.cvtB2IB 60: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 60: [ RUN ] SimdScalarTest.cvtIB2B 60: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 60: [ RUN ] SimdScalarTest.expandScalarsToTriplets 60: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 60: [----------] 41 tests from SimdScalarTest (0 ms total) 60: 60: [----------] 8 tests from SimdScalarUtilTest 60: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 60: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 60: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 60: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 60: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 60: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 60: 60: [----------] 37 tests from SimdScalarMathTest 60: [ RUN ] SimdScalarMathTest.copysign 60: [ OK ] SimdScalarMathTest.copysign (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPair 60: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 60: [ RUN ] SimdScalarMathTest.inv 60: [ OK ] SimdScalarMathTest.inv (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrt 60: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdScalarMathTest.log 60: [ OK ] SimdScalarMathTest.log (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2 60: [ OK ] SimdScalarMathTest.exp2 (0 ms) 60: [ RUN ] SimdScalarMathTest.exp 60: [ OK ] SimdScalarMathTest.exp (0 ms) 60: [ RUN ] SimdScalarMathTest.erf 60: [ OK ] SimdScalarMathTest.erf (0 ms) 60: [ RUN ] SimdScalarMathTest.erfc 60: [ OK ] SimdScalarMathTest.erfc (0 ms) 60: [ RUN ] SimdScalarMathTest.sincos 60: [ OK ] SimdScalarMathTest.sincos (0 ms) 60: [ RUN ] SimdScalarMathTest.sin 60: [ OK ] SimdScalarMathTest.sin (0 ms) 60: [ RUN ] SimdScalarMathTest.cos 60: [ OK ] SimdScalarMathTest.cos (0 ms) 60: [ RUN ] SimdScalarMathTest.tan 60: [ OK ] SimdScalarMathTest.tan (0 ms) 60: [ RUN ] SimdScalarMathTest.asin 60: [ OK ] SimdScalarMathTest.asin (0 ms) 60: [ RUN ] SimdScalarMathTest.acos 60: [ OK ] SimdScalarMathTest.acos (0 ms) 60: [ RUN ] SimdScalarMathTest.atan 60: [ OK ] SimdScalarMathTest.atan (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2 60: [ OK ] SimdScalarMathTest.atan2 (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrection 60: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 60: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.invSingleAccuracy 60: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 60: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.logSingleAccuracy 60: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 60: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.expSingleAccuracy 60: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 60: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 60: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 60: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 60: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 60: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 60: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 60: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 60: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 37 tests from SimdScalarMathTest (0 ms total) 60: 60: [----------] 1 test from SimdTest 60: [ RUN ] SimdTest.GmxAligned 60: [ OK ] SimdTest.GmxAligned (0 ms) 60: [----------] 1 test from SimdTest (0 ms total) 60: 60: [----------] 42 tests from SimdFloatingpointTest 60: [ RUN ] SimdFloatingpointTest.setZero 60: [ OK ] SimdFloatingpointTest.setZero (0 ms) 60: [ RUN ] SimdFloatingpointTest.set 60: [ OK ] SimdFloatingpointTest.set (0 ms) 60: [ RUN ] SimdFloatingpointTest.add 60: [ OK ] SimdFloatingpointTest.add (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskAdd 60: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 60: [ RUN ] SimdFloatingpointTest.sub 60: [ OK ] SimdFloatingpointTest.sub (0 ms) 60: [ RUN ] SimdFloatingpointTest.mul 60: [ OK ] SimdFloatingpointTest.mul (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzMul 60: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 60: [ RUN ] SimdFloatingpointTest.fma 60: [ OK ] SimdFloatingpointTest.fma (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzFma 60: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fms 60: [ OK ] SimdFloatingpointTest.fms (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnma 60: [ OK ] SimdFloatingpointTest.fnma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnms 60: [ OK ] SimdFloatingpointTest.fnms (0 ms) 60: [ RUN ] SimdFloatingpointTest.abs 60: [ OK ] SimdFloatingpointTest.abs (0 ms) 60: [ RUN ] SimdFloatingpointTest.neg 60: [ OK ] SimdFloatingpointTest.neg (0 ms) 60: [ RUN ] SimdFloatingpointTest.and 60: [ OK ] SimdFloatingpointTest.and (0 ms) 60: [ RUN ] SimdFloatingpointTest.or 60: [ OK ] SimdFloatingpointTest.or (0 ms) 60: [ RUN ] SimdFloatingpointTest.xor 60: [ OK ] SimdFloatingpointTest.xor (0 ms) 60: [ RUN ] SimdFloatingpointTest.andNot 60: [ OK ] SimdFloatingpointTest.andNot (0 ms) 60: [ RUN ] SimdFloatingpointTest.max 60: [ OK ] SimdFloatingpointTest.max (0 ms) 60: [ RUN ] SimdFloatingpointTest.min 60: [ OK ] SimdFloatingpointTest.min (0 ms) 60: [ RUN ] SimdFloatingpointTest.round 60: [ OK ] SimdFloatingpointTest.round (0 ms) 60: [ RUN ] SimdFloatingpointTest.roundMode 60: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 60: [ RUN ] SimdFloatingpointTest.trunc 60: [ OK ] SimdFloatingpointTest.trunc (0 ms) 60: [ RUN ] SimdFloatingpointTest.frexp 60: [ OK ] SimdFloatingpointTest.frexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.ldexp 60: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.rsqrt 60: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRsqrt 60: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.rcp 60: [ OK ] SimdFloatingpointTest.rcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRcp 60: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 60: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.selectByNotMask 60: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpNe 60: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLe 60: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLt 60: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 60: [ RUN ] SimdFloatingpointTest.testBits 60: [ OK ] SimdFloatingpointTest.testBits (0 ms) 60: [ RUN ] SimdFloatingpointTest.andB 60: [ OK ] SimdFloatingpointTest.andB (0 ms) 60: [ RUN ] SimdFloatingpointTest.orB 60: [ OK ] SimdFloatingpointTest.orB (0 ms) 60: [ RUN ] SimdFloatingpointTest.anyTrueB 60: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 60: [ RUN ] SimdFloatingpointTest.blend 60: [ OK ] SimdFloatingpointTest.blend (0 ms) 60: [ RUN ] SimdFloatingpointTest.reduce 60: [ OK ] SimdFloatingpointTest.reduce (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 60: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 60: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 60: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 60: 60: [----------] 16 tests from SimdFloatingpointUtilTest 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 60: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 60: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 60: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 60: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 60: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 60: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 60: 60: [----------] 23 tests from SimdIntegerTest 60: [ RUN ] SimdIntegerTest.setZero 60: [ OK ] SimdIntegerTest.setZero (0 ms) 60: [ RUN ] SimdIntegerTest.set 60: [ OK ] SimdIntegerTest.set (0 ms) 60: [ RUN ] SimdIntegerTest.add 60: [ OK ] SimdIntegerTest.add (0 ms) 60: [ RUN ] SimdIntegerTest.sub 60: [ OK ] SimdIntegerTest.sub (0 ms) 60: [ RUN ] SimdIntegerTest.mul 60: [ OK ] SimdIntegerTest.mul (0 ms) 60: [ RUN ] SimdIntegerTest.and 60: [ OK ] SimdIntegerTest.and (0 ms) 60: [ RUN ] SimdIntegerTest.andNot 60: [ OK ] SimdIntegerTest.andNot (0 ms) 60: [ RUN ] SimdIntegerTest.or 60: [ OK ] SimdIntegerTest.or (0 ms) 60: [ RUN ] SimdIntegerTest.xor 60: [ OK ] SimdIntegerTest.xor (0 ms) 60: [ RUN ] SimdIntegerTest.extract 60: [ OK ] SimdIntegerTest.extract (0 ms) 60: [ RUN ] SimdIntegerTest.cvtR2I 60: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvttR2I 60: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvtI2R 60: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpLt 60: [ OK ] SimdIntegerTest.cmpLt (0 ms) 60: [ RUN ] SimdIntegerTest.testBits 60: [ OK ] SimdIntegerTest.testBits (0 ms) 60: [ RUN ] SimdIntegerTest.andB 60: [ OK ] SimdIntegerTest.andB (0 ms) 60: [ RUN ] SimdIntegerTest.orB 60: [ OK ] SimdIntegerTest.orB (0 ms) 60: [ RUN ] SimdIntegerTest.anyTrue 60: [ OK ] SimdIntegerTest.anyTrue (0 ms) 60: [ RUN ] SimdIntegerTest.blend 60: [ OK ] SimdIntegerTest.blend (0 ms) 60: [ RUN ] SimdIntegerTest.cvtB2IB 60: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 60: [ RUN ] SimdIntegerTest.cvtIB2B 60: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 60: [----------] 23 tests from SimdIntegerTest (0 ms total) 60: 60: [----------] 56 tests from SimdMathTest 60: [ RUN ] SimdMathTest.generateTestPointsFloat 60: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 60: [ RUN ] SimdMathTest.copysign 60: [ OK ] SimdMathTest.copysign (0 ms) 60: [ RUN ] SimdMathTest.invsqrt 60: [ OK ] SimdMathTest.invsqrt (0 ms) 60: [ RUN ] SimdMathTest.maskzInvsqrt 60: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPair 60: [ OK ] SimdMathTest.invsqrtPair (0 ms) 60: [ RUN ] SimdMathTest.sqrt 60: [ OK ] SimdMathTest.sqrt (0 ms) 60: [ RUN ] SimdMathTest.sqrtUnsafe 60: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 60: [ RUN ] SimdMathTest.inv 60: [ OK ] SimdMathTest.inv (1 ms) 60: [ RUN ] SimdMathTest.maskzInv 60: [ OK ] SimdMathTest.maskzInv (0 ms) 60: [ RUN ] SimdMathTest.cbrt 60: [ OK ] SimdMathTest.cbrt (0 ms) 60: [ RUN ] SimdMathTest.invcbrt 60: [ OK ] SimdMathTest.invcbrt (0 ms) 60: [ RUN ] SimdMathTest.log2 60: [ OK ] SimdMathTest.log2 (0 ms) 60: [ RUN ] SimdMathTest.log 60: [ OK ] SimdMathTest.log (0 ms) 60: [ RUN ] SimdMathTest.exp2 60: [ OK ] SimdMathTest.exp2 (0 ms) 60: [ RUN ] SimdMathTest.exp2Unsafe 60: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 60: [ RUN ] SimdMathTest.exp 60: [ OK ] SimdMathTest.exp (0 ms) 60: [ RUN ] SimdMathTest.expUnsafe 60: [ OK ] SimdMathTest.expUnsafe (0 ms) 60: [ RUN ] SimdMathTest.pow 60: [ OK ] SimdMathTest.pow (0 ms) 60: [ RUN ] SimdMathTest.powUnsafe 60: [ OK ] SimdMathTest.powUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erf 60: [ OK ] SimdMathTest.erf (0 ms) 60: [ RUN ] SimdMathTest.erfc 60: [ OK ] SimdMathTest.erfc (0 ms) 60: [ RUN ] SimdMathTest.sin 60: [ OK ] SimdMathTest.sin (0 ms) 60: [ RUN ] SimdMathTest.cos 60: [ OK ] SimdMathTest.cos (0 ms) 60: [ RUN ] SimdMathTest.tan 60: [ OK ] SimdMathTest.tan (0 ms) 60: [ RUN ] SimdMathTest.asin 60: [ OK ] SimdMathTest.asin (0 ms) 60: [ RUN ] SimdMathTest.acos 60: [ OK ] SimdMathTest.acos (0 ms) 60: [ RUN ] SimdMathTest.atan 60: [ OK ] SimdMathTest.atan (0 ms) 60: [ RUN ] SimdMathTest.atan2 60: [ OK ] SimdMathTest.atan2 (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrection 60: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrection 60: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracy 60: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.invSingleAccuracy 60: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) 60: [ RUN ] SimdMathTest.cbrtSingleAccuracy 60: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 60: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.log2SingleAccuracy 60: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.logSingleAccuracy 60: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracy 60: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 60: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracy 60: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracy 60: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erfSingleAccuracy 60: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.erfcSingleAccuracy 60: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sinSingleAccuracy 60: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.cosSingleAccuracy 60: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.tanSingleAccuracy 60: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.asinSingleAccuracy 60: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.acosSingleAccuracy 60: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atanSingleAccuracy 60: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atan2SingleAccuracy 60: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 56 tests from SimdMathTest (22 ms total) 60: 60: [----------] 1 test from EmptyArrayRefTest 60: [ RUN ] EmptyArrayRefTest.IsEmpty 60: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 60: [----------] 1 test from EmptyArrayRefTest (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/0.Assignment 60: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/1.Assignment 60: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/0.Basic 60: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/1.Basic 60: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 60: 60: [----------] 3 tests from SimdVectorOperationsTest 60: [ RUN ] SimdVectorOperationsTest.iprod 60: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 60: [ RUN ] SimdVectorOperationsTest.norm2 60: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 60: [ RUN ] SimdVectorOperationsTest.cprod 60: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 60: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 60: 60: [----------] 32 tests from Simd4FloatingpointTest 60: [ RUN ] Simd4FloatingpointTest.setZero 60: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 60: [ RUN ] Simd4FloatingpointTest.set 60: [ OK ] Simd4FloatingpointTest.set (0 ms) 60: [ RUN ] Simd4FloatingpointTest.add 60: [ OK ] Simd4FloatingpointTest.add (0 ms) 60: [ RUN ] Simd4FloatingpointTest.sub 60: [ OK ] Simd4FloatingpointTest.sub (0 ms) 60: [ RUN ] Simd4FloatingpointTest.mul 60: [ OK ] Simd4FloatingpointTest.mul (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fma 60: [ OK ] Simd4FloatingpointTest.fma (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fms 60: [ OK ] Simd4FloatingpointTest.fms (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fnma 60: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fnms 60: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 60: [ RUN ] Simd4FloatingpointTest.abs 60: [ OK ] Simd4FloatingpointTest.abs (0 ms) 60: [ RUN ] Simd4FloatingpointTest.neg 60: [ OK ] Simd4FloatingpointTest.neg (0 ms) 60: [ RUN ] Simd4FloatingpointTest.and 60: [ OK ] Simd4FloatingpointTest.and (0 ms) 60: [ RUN ] Simd4FloatingpointTest.or 60: [ OK ] Simd4FloatingpointTest.or (0 ms) 60: [ RUN ] Simd4FloatingpointTest.xor 60: [ OK ] Simd4FloatingpointTest.xor (0 ms) 60: [ RUN ] Simd4FloatingpointTest.andNot 60: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 60: [ RUN ] Simd4FloatingpointTest.max 60: [ OK ] Simd4FloatingpointTest.max (0 ms) 60: [ RUN ] Simd4FloatingpointTest.min 60: [ OK ] Simd4FloatingpointTest.min (0 ms) 60: [ RUN ] Simd4FloatingpointTest.round 60: [ OK ] Simd4FloatingpointTest.round (0 ms) 60: [ RUN ] Simd4FloatingpointTest.trunc 60: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 60: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 60: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 60: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 60: [ RUN ] Simd4FloatingpointTest.selectByNotMask 60: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpNe 60: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpLe 60: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpLt 60: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 60: [ RUN ] Simd4FloatingpointTest.andB 60: [ OK ] Simd4FloatingpointTest.andB (0 ms) 60: [ RUN ] Simd4FloatingpointTest.orB 60: [ OK ] Simd4FloatingpointTest.orB (0 ms) 60: [ RUN ] Simd4FloatingpointTest.anyTrue 60: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 60: [ RUN ] Simd4FloatingpointTest.blend 60: [ OK ] Simd4FloatingpointTest.blend (0 ms) 60: [ RUN ] Simd4FloatingpointTest.reduce 60: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 60: [ RUN ] Simd4FloatingpointTest.dotProduct 60: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 60: [ RUN ] Simd4FloatingpointTest.transpose 60: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 60: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 60: 60: [----------] 2 tests from Simd4MathTest 60: [ RUN ] Simd4MathTest.invsqrt 60: [ OK ] Simd4MathTest.invsqrt (0 ms) 60: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 60: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 60: [----------] 2 tests from Simd4MathTest (0 ms total) 60: 60: [----------] 1 test from Simd4VectorOperationsTest 60: [ RUN ] Simd4VectorOperationsTest.norm2 60: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 60: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 288 tests from 22 test suites ran. (23 ms total) 60: [ PASSED ] 288 tests. 60/104 Test #60: SimdUnitTests ............................. Passed 0.04 sec test 61 Start 61: CompatibilityHelpersTests 61: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/compat/tests 61: Test timeout computed to be: 30 61: [==========] Running 9 tests from 6 test suites. 61: [----------] Global test environment set-up. 61: [----------] 4 tests from TemplateMPTest 61: [ RUN ] TemplateMPTest.MpWithIndexInt 61: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexIntBad 61: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexBool 61: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexEnum 61: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 61: [----------] 4 tests from TemplateMPTest (0 ms total) 61: 61: [----------] 1 test from NotNullConstruction 61: [ RUN ] NotNullConstruction.Works 61: [ OK ] NotNullConstruction.Works (0 ms) 61: [----------] 1 test from NotNullConstruction (0 ms total) 61: 61: [----------] 1 test from NotNullCasting 61: [ RUN ] NotNullCasting.Works 61: [ OK ] NotNullCasting.Works (0 ms) 61: [----------] 1 test from NotNullCasting (0 ms total) 61: 61: [----------] 1 test from NotNullAssignment 61: [ RUN ] NotNullAssignment.Works 61: [ OK ] NotNullAssignment.Works (0 ms) 61: [----------] 1 test from NotNullAssignment (0 ms total) 61: 61: [----------] 1 test from MakeNotNull 61: [ RUN ] MakeNotNull.Works 61: [ OK ] MakeNotNull.Works (0 ms) 61: [----------] 1 test from MakeNotNull (0 ms total) 61: 61: [----------] 1 test from NotNull 61: [ RUN ] NotNull.WorksInContainers 61: [ OK ] NotNull.WorksInContainers (0 ms) 61: [----------] 1 test from NotNull (0 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 9 tests from 6 test suites ran. (0 ms total) 61: [ PASSED ] 9 tests. 61/104 Test #61: CompatibilityHelpersTests ................. Passed 0.01 sec test 62 Start 62: GmxAnaTest 62: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GmxAnaTest.xml" 62: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests 62: Test timeout computed to be: 600 62: [==========] Running 37 tests from 10 test suites. 62: [----------] Global test environment set-up. 62: [----------] 7 tests from Entropy 62: [ RUN ] Entropy.Schlitter_300_NoLinear 62: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 62: [ RUN ] Entropy.Schlitter_300_Linear 62: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_Linear 62: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 62: [ RUN ] Entropy.EntropyCompare_200_Linear 62: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 62: [ RUN ] Entropy.EntropyCompare_300_Linear 62: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 62: [----------] 7 tests from Entropy (0 ms total) 62: 62: [----------] 2 tests from GmxChiTest 62: [ RUN ] GmxChiTest.gmxchiWorksWithAll 62: Analyzing from residue 1 to residue 11 62: 10 residues with dihedrals found 62: 46 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 46 62: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithAll (390 ms) 62: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 62: Analyzing from residue 2 to residue 6 62: 5 residues with dihedrals found 62: 23 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 23 62: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (175 ms) 62: [----------] 2 tests from GmxChiTest (629 ms total) 62: 62: [----------] 10 tests from MindistTest 62: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistWorksWithSingleAtoms (5 ms) 62: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 62: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 62: [ RUN ] MindistTest.mindistPicksUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 62: [ RUN ] MindistTest.ngWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.ngWorks (0 ms) 62: [ RUN ] MindistTest.groupWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.groupWorks (1 ms) 62: [ RUN ] MindistTest.maxDistWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.maxDistWorks (0 ms) 62: [ RUN ] MindistTest.noPbcWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.noPbcWorks (0 ms) 62: [ RUN ] MindistTest.resPerTimeWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.resPerTimeWorks (0 ms) 62: [ RUN ] MindistTest.matrixWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 5: 'atoms123' 62: Special case: making distance matrix between all atoms in group atoms123 62: [ OK ] MindistTest.matrixWorks (0 ms) 62: [----------] 10 tests from MindistTest (11 ms total) 62: 62: [----------] 1 test from GmxRmsTest 62: [ RUN ] GmxRmsTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Select group for least squares fit 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Select group for RMSD calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to -603985335 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 1: 'Protein' 62: Selected 1: 'Protein' 62: [ OK ] GmxRmsTest.BasicOutputWorks (197 ms) 62: [----------] 1 test from GmxRmsTest (197 ms total) 62: 62: [----------] 1 test from GmxRmsdistTest 62: [ RUN ] GmxRmsdistTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: 62: rmsmax = 0.382568, rmscmax = 0.659498 62: Setting the LD random seed to -46729233 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 0: 'System' 62: [ OK ] GmxRmsdistTest.BasicOutputWorks (198 ms) 62: [----------] 1 test from GmxRmsdistTest (198 ms total) 62: 62: [----------] 1 test from GmxRmsfTest 62: [ RUN ] GmxRmsfTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Select group(s) for root mean square calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to -172426497 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 3: 'C-alpha' 62: [ OK ] GmxRmsfTest.BasicOutputWorks (191 ms) 62: [----------] 1 test from GmxRmsfTest (191 ms total) 62: 62: [----------] 1 test from GmxSorientTest 62: [ RUN ] GmxSorientTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Group 0 ( System) has 923 elements 62: Group 1 ( Protein) has 29 elements 62: Group 2 ( Protein-H) has 17 elements 62: Group 3 ( C-alpha) has 2 elements 62: Group 4 ( Backbone) has 6 elements 62: Group 5 ( MainChain) has 9 elements 62: Group 6 ( MainChain+Cb) has 11 elements 62: Group 7 ( MainChain+H) has 13 elements 62: Group 8 ( SideChain) has 16 elements 62: Group 9 ( SideChain-H) has 8 elements 62: Group 10 ( Prot-Masses) has 23 elements 62: Group 11 ( non-Protein) has 894 elements 62: Group 12 ( Water) has 894 elements 62: Group 13 ( SOL) has 894 elements 62: Group 14 ( non-Water) has 29 elements 62: Select a group: Select a group: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Average nr of molecules between 0 and 0.5 nm: 13.0 62: Average cos(theta1) between 0 and 0.5 nm: 0.103 62: Average 3cos2(theta2)-1 between 0 and 0.5 nm: -0.098 62: Setting the LD random seed to -1141048969 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.pdb', all velocities are zero 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: Analysing residue names: 62: There are: 2 Protein residues 62: There are: 298 Water residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Select a group of reference particles and a solvent group: 62: Selected 1: 'Protein' 62: Selected 12: 'Water' 62: [ OK ] GmxSorientTest.BasicOutputWorks (15 ms) 62: [----------] 1 test from GmxSorientTest (15 ms total) 62: 62: [----------] 1 test from GmxRotmatTest 62: [ RUN ] GmxRotmatTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Setting the LD random seed to -9122886 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 4: 'Backbone' 62: [ OK ] GmxRotmatTest.BasicOutputWorks (192 ms) 62: [----------] 1 test from GmxRotmatTest (192 ms total) 62: 62: [----------] 1 test from GmxSaltbrTest 62: [ RUN ] GmxSaltbrTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Setting the LD random seed to -556929105 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: This run will generate roughly 0 Mb of data 62: CG: SOL1-1 Q: -0.834 Atoms: 0 62: CG: SOL1-2 Q: 0.417 Atoms: 1 62: CG: SOL1-3 Q: 0.417 Atoms: 2 62: CG: SOL2-4 Q: -0.834 Atoms: 3 62: CG: SOL2-5 Q: 0.417 Atoms: 4 62: CG: SOL2-6 Q: 0.417 Atoms: 5 62: [ OK ] GmxSaltbrTest.BasicOutputWorks (3 ms) 62: [----------] 1 test from GmxSaltbrTest (3 ms total) 62: 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (11 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 37 tests from 10 test suites ran. (1452 ms total) 62: [ PASSED ] 37 tests. 62/104 Test #62: GmxAnaTest ................................ Passed 1.47 sec test 63 Start 63: GmxPreprocessTests 63: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests 63: Test timeout computed to be: 1920 63: [==========] Running 282 tests from 17 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertInteractionsTest 63: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 63: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 63: [----------] 1 test from ConvertInteractionsTest (0 ms total) 63: 63: [----------] 5 tests from GenconfTest 63: [ RUN ] GenconfTest.nbox_Works 63: [ OK ] GenconfTest.nbox_Works (0 ms) 63: [ RUN ] GenconfTest.nbox_norenumber_Works 63: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 63: [ RUN ] GenconfTest.nbox_dist_Works 63: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 63: [ RUN ] GenconfTest.nbox_rot_Works 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 63: [ RUN ] GenconfTest.trj_Works 63: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 63: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Last frame 3 time 3.000 63: [ OK ] GenconfTest.trj_Works (0 ms) 63: [----------] 5 tests from GenconfTest (2 ms total) 63: 63: [----------] 2 tests from GenionTest 63: [ RUN ] GenionTest.HighConcentrationIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Group 0 ( System) has 653 elements 63: Group 1 ( Water) has 648 elements 63: Group 2 ( SOL) has 648 elements 63: Group 3 ( non-Water) has 5 elements 63: Group 4 ( Other) has 5 elements 63: Group 5 ( METH) has 5 elements 63: Select a group: Number of (3-atomic) solvent molecules: 216 63: Using random seed 1997. 63: Replacing solvent molecule 56 (atom 168) with NA 63: Replacing solvent molecule 120 (atom 360) with NA 63: Replacing solvent molecule 182 (atom 546) with NA 63: Replacing solvent molecule 71 (atom 213) with NA 63: Replacing solvent molecule 189 (atom 567) with CL 63: Replacing solvent molecule 54 (atom 162) with CL 63: Replacing solvent molecule 155 (atom 465) with CL 63: Replacing solvent molecule 99 (atom 297) with CL 63: 63: Setting the LD random seed to 330823546 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: Will try to add 4 NA ions and 4 CL ions. 63: Select a continuous group of solvent molecules 63: Selected 1: 'Water' 63: [ OK ] GenionTest.HighConcentrationIonPlacement (212 ms) 63: [ RUN ] GenionTest.NoIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: No ions to add, will just copy input configuration. 63: Setting the LD random seed to -321327165 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GenionTest.NoIonPlacement (235 ms) 63: [----------] 2 tests from GenionTest (448 ms total) 63: 63: [----------] 1 test from GenRestrTest 63: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 63: 63: Reading structure file 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Select group to position restrain 63: Selected 3: 'C-alpha' 63: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 63: [----------] 1 test from GenRestrTest (1 ms total) 63: 63: [----------] 9 tests from PreprocessingAtomTypesTest 63: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 63: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 63: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 63: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 63: 63: [----------] 10 tests from PreprocessingBondAtomTypeTest 63: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 63: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 63: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 63: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 63: 63: [----------] 3 tests from GromppDirectiveTest 63: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to 1073608703 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2121263802 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (61 ms) 63: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 63: coefficients that do not sum to zero. This does not affect the simulation 63: and can be ignored, unless you are comparing potential energy values with 63: other force field ports and/or MD software. 63: First such dihedral in molecule A, involving atoms 0 2 1 3 63: 63: 63: NOTE 2 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to 1073462637 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -303563025 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (15 ms) 63: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 63: Setting the LD random seed to -21661761 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -67115587 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (239 ms) 63: [----------] 3 tests from GromppDirectiveTest (316 ms total) 63: 63: [----------] 6 tests from InsertMoleculesTest 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: 63: Added 1 molecules (out of 1 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 63: 63: Output configuration contains 8 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (0 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: Try 2 success (now 10 atoms)! 63: 63: Added 2 molecules (out of 2 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 63: 63: Output configuration contains 10 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 650 atoms)! 63: Try 2 success (now 652 atoms)! 63: Try 3 success (now 654 atoms)! 63: Try 4 success (now 656 atoms)! 63: 63: Added 4 molecules (out of 4 requested) 63: Replaced 8 residues (24 atoms) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 63: 63: Output configuration contains 632 atoms in 212 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (2 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Read 4 positions from file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 63: 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 63: Try 13 success (now 6 atoms)! 63: 63: Added 3 molecules (out of 4 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 63: 63: Output configuration contains 6 atoms in 3 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (0 ms) 63: [----------] 6 tests from InsertMoleculesTest (6 ms total) 63: 63: [----------] 3 tests from MassRepartitioning 63: [ RUN ] MassRepartitioning.ValidCaseWorks 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 63: [ RUN ] MassRepartitioning.UnboundGivesWarning 63: 63: WARNING 1 [file unknown]: 63: The are 1 atoms that have a mass below the mass repartitioning limit but 63: are not bound. These masses cannot be repartitioned. 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 63: [ RUN ] MassRepartitioning.LightPartnerGivesError 63: 63: ERROR 1 [file unknown]: 63: Light atoms are bound to at least one atom that has a too low mass for 63: repartitioning 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 63: [----------] 3 tests from MassRepartitioning (0 ms total) 63: 63: [----------] 36 tests from GetIrTest 63: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 63: Ignoring obsolete mdp entry 'title' 63: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) 63: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 63: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (3 ms) 63: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) 63: [ RUN ] GetIrTest.RejectsValueWithoutKey 63: [ OK ] GetIrTest.RejectsValueWithoutKey (3 ms) 63: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 63: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (3 ms) 63: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 63: [ RUN ] GetIrTest.AcceptsEmptyLines 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstpcouple 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: With multiple time stepping, nstpcouple should be a multiple of 63: mts-factor 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: The Berendsen barostat does not generate any strictly correct ensemble, 63: and should not be used for new production simulations (in our opinion). 63: We recommend using the C-rescale barostat instead. 63: 63: 63: ERROR 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: compressibility must be > 0 when using pressure coupling Berendsen 63: 63: 63: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstdhdl 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstdhdl (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Lambda state must be set, either with init-lambda-state or with 63: init-lambda 63: 63: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 63: [ RUN ] GetIrTest.MtsCheckSDNotSupported 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: Multiple time stepping is only supported with integrator md 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 63: [ RUN ] GetIrTest.AcceptsElectricField 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricField (1 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 63: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 63: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (1 ms) 63: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 63: [ RUN ] GetIrTest.RejectsImplicitSolventYes 63: [ OK ] GetIrTest.RejectsImplicitSolventYes (3 ms) 63: [ RUN ] GetIrTest.AcceptsMimic 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsMimic (1 ms) 63: [ RUN ] GetIrTest.AcceptsTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 63: pull-coord2 has a non-zero force constant and is also referenced in 63: pull-coord1-expression. Make sure that this is intended. In most use 63: cases, the pull coordinates referenced by a transformation coordinate 63: should have their force constant set to zero. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 63: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 63: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 63: pull-coord2 can not use pull-coord1 in the transformation since this is a 63: constraint 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 63: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 63: [ RUN ] GetIrTest.MissingTransformationCoordExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 63: pull-coord1-expression not set for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 63: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 63: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 63: in total 100001 steps. This is not compatible with using soft-core 63: potentials. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 63: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.AcceptsFmmOptions 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsFmmOptions_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsFmmOptions (1 ms) 63: [----------] 36 tests from GetIrTest (63 ms total) 63: 63: [----------] 6 tests from SolvateTest 63: [ RUN ] SolvateTest.cs_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 1x1x1 boxes 63: Solvent box contains 270 atoms in 90 residues 63: Removed 129 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 47 residues 63: Generated solvent containing 141 atoms in 47 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 63: 63: Output configuration contains 141 atoms in 47 residues 63: Volume : 1.331 (nm^3) 63: Density : 1056.36 (g/l) 63: Number of solvent molecules: 47 63: 63: [ OK ] SolvateTest.cs_box_Works (2 ms) 63: [ RUN ] SolvateTest.cs_cp_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: [ OK ] SolvateTest.cs_cp_Works (11 ms) 63: [ RUN ] SolvateTest.cs_cp_p_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: Processing topology 63: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 63: [ OK ] SolvateTest.cs_cp_p_Works (11 ms) 63: [ RUN ] SolvateTest.shell_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 1902 solvent atoms more than 1.000000 nm from solute. 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 252 residues 63: Generated solvent containing 756 atoms in 252 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 63: 63: Output configuration contains 762 atoms in 254 residues 63: Volume : 27.2709 (nm^3) 63: Density : 279.3 (g/l) 63: Number of solvent molecules: 252 63: 63: [ OK ] SolvateTest.shell_Works (6 ms) 63: [ RUN ] SolvateTest.update_Topology_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 3x3x3 boxes 63: Solvent box contains 14952 atoms in 4984 residues 63: Removed 2787 solvent atoms due to solvent-solvent overlap 63: Removed 30 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 2 different molecule types: 63: HOH ( 3 atoms): 1876 residues 63: SOL ( 3 atoms): 2169 residues 63: Generated solvent containing 0 atoms in 0 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 63: 63: Output configuration contains 12141 atoms in 4047 residues 63: Volume : 125 (nm^3) 63: Density : 968.963 (g/l) 63: Number of solvent molecules: 4045 63: 63: Processing topology 63: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: [ OK ] SolvateTest.update_Topology_Works (46 ms) 63: [ RUN ] SolvateTest.cs_pdb_big_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 1218 atoms in 406 residues 63: Removed 555 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 221 residues 63: Generated solvent containing 663 atoms in 221 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 63: 63: Output configuration contains 663 atoms in 221 residues 63: Volume : 8 (nm^3) 63: Density : 826.409 (g/l) 63: Number of solvent molecules: 221 63: 63: [ OK ] SolvateTest.cs_pdb_big_box_Works (4 ms) 63: [----------] 6 tests from SolvateTest (83 ms total) 63: 63: [----------] 1 test from TopDirTests 63: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 63: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 63: [----------] 1 test from TopDirTests (0 ms total) 63: 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (1 ms total) 63: 63: [----------] 45 tests from SinglePeptideFragments/EditconfTest 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (5 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.42 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.42 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.42 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.28 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.28 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.28 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (0 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (1 ms) 63: [----------] 45 tests from SinglePeptideFragments/EditconfTest (69 ms total) 63: 63: [----------] 16 tests from CorrectVelocity/MaxwellTest 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 63: [----------] 16 tests from CorrectVelocity/MaxwellTest (7 ms total) 63: 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1478640679 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -524361 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -81407068 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2063200451 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to 956194191 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -537534604 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -21282835 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1727832051 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1311763 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2126118431 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1157679620 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -85495942 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -537952513 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -459298 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1625315617 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -847364421 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1355056148 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1375736074 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1352031515 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -102039681 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1075862467 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -553661619 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -614666377 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 931135447 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -21046273 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1361060865 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -21628929 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -8438021 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -1082148033 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -671238659 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -704716993 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -919561 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -387035393 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -167904289 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to -33555217 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -50532353 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 63: Setting the LD random seed to 1608767214 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -393219 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 (2 ms) 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest (52 ms total) 63: 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 63: Setting the LD random seed to -295703875 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 63: Setting the LD random seed to 1738133503 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to 2143223479 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1547675390 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -71335953 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -46 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -595600457 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -19108490 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -549490054 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -855867395 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 63: Setting the LD random seed to 1811529071 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 63: Setting the LD random seed to 2096027231 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -16847876 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 63: Setting the LD random seed to 1577052095 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 63: Setting the LD random seed to -10485801 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -805306577 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 63: Setting the LD random seed to -620969995 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1543534081 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 63: Setting the LD random seed to -90121 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -141231121 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 63: Setting the LD random seed to -807939073 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -571016515 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 63: Setting the LD random seed to -32195841 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2013257716 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 63: Setting the LD random seed to -537396739 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -840040497 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 63: Setting the LD random seed to 2079841109 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1434449818 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -527175745 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -637534531 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -675973141 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -16787515 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 63: Setting the LD random seed to -541077799 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 63: Setting the LD random seed to -135332865 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -172142721 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 63: Setting the LD random seed to 1811655582 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -872425121 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -319357065 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 63: Setting the LD random seed to -9177126 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (3 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 63: Setting the LD random seed to 2096889327 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2129653499 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 (4 ms) 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest (93 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 282 tests from 17 test suites ran. (1146 ms total) 63: [ PASSED ] 242 tests. 63: [ SKIPPED ] 40 tests, listed below: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63/104 Test #63: GmxPreprocessTests ........................ Passed 1.16 sec test 64 Start 64: Pdb2gmx1Test 64: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 64: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests 64: Test timeout computed to be: 1920 64: [==========] Running 30 tests from 1 test suite. 64: [----------] Global test environment set-up. 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (16 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (12 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (16 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (12 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (36 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (44 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (16 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (38 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (16 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest (605 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 30 tests from 1 test suite ran. (605 ms total) 64: [ PASSED ] 30 tests. 64/104 Test #64: Pdb2gmx1Test .............................. Passed 0.62 sec test 65 Start 65: Pdb2gmx2Test 65: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 65: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests 65: Test timeout computed to be: 1920 65: [==========] Running 40 tests from 2 test suites. 65: [----------] Global test environment set-up. 65: [----------] 20 tests from G43a1/Pdb2gmxTest 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (15 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (32 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (33 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (31 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (34 ms) 65: [----------] 20 tests from G43a1/Pdb2gmxTest (420 ms total) 65: 65: [----------] 20 tests from G53a6/Pdb2gmxTest 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (36 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (34 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (34 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (34 ms) 65: [----------] 20 tests from G53a6/Pdb2gmxTest (449 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 40 tests from 2 test suites ran. (869 ms total) 65: [ PASSED ] 40 tests. 65/104 Test #65: Pdb2gmx2Test .............................. Passed 0.88 sec test 66 Start 66: Pdb2gmx3Test 66: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 66: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/gmxpreprocess/tests 66: Test timeout computed to be: 1920 66: [==========] Running 55 tests from 9 test suites. 66: [----------] Global test environment set-up. 66: [----------] 10 tests from Amber/Pdb2gmxTest 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (45 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (46 ms) 66: [----------] 10 tests from Amber/Pdb2gmxTest (244 ms total) 66: 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest 66: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber99sb-ildn force field and the tip4p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (9 ms) 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest (9 ms total) 66: 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (37 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (37 ms) 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest (193 ms total) 66: 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the opc water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (6 ms) 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the tip4pew water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (6 ms) 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest (12 ms total) 66: 66: [----------] 12 tests from Charmm/Pdb2gmxTest 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 0 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (9 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 8 virtual sites 66: Added 2 dummy masses 66: Added 3 new constraints 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 9 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (9 ms) 66: [----------] 12 tests from Charmm/Pdb2gmxTest (245 ms total) 66: 66: [----------] 8 tests from ChainSep/Pdb2gmxTest 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (16 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 7 acceptors were found. 66: There are 7 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS8 66: NE223 66: MET12 SD55 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 317 pairs 66: Before cleaning: 322 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 7 58 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (58 atoms, 7 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 124 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 125, now 125 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 5 cmap torsion pairs 66: 66: There are 322 dihedrals, 19 impropers, 227 angles 66: 314 pairs, 125 bonds and 0 virtual sites 66: 66: Total mass 846.083 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 124 atoms 7 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (15 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (16 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 12 acceptors were found. 66: There are 13 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 66: SG9 66: HIS8 NE251 1.055 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 288 pairs 66: Before cleaning: 293 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 8 61 66: 66: 2 'B' 3 25 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (61 atoms, 8 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 8 residues with 114 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 115, now 115 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6 cmap torsion pairs 66: 66: There are 293 dihedrals, 23 impropers, 203 angles 66: 285 pairs, 115 bonds and 0 virtual sites 66: 66: Total mass 888.952 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 114 atoms 8 residues 66: 66: Including chain 2 in system: 61 atoms 3 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (15 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 650 pairs 66: Before cleaning: 660 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 3 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 261 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 260, now 260 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 8 cmap torsion pairs 66: 66: There are 660 dihedrals, 45 impropers, 466 angles 66: 647 pairs, 260 bonds and 0 virtual sites 66: 66: Total mass 1900.162 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (17 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 6 donors and 4 acceptors were found. 66: There are 3 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 164 pairs 66: Before cleaning: 169 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 4 33 66: 66: 3 'B' 3 25 66: 66: 4 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (33 atoms, 4 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 66 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 67, now 67 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 169 dihedrals, 13 impropers, 118 angles 66: 161 pairs, 67 bonds and 0 virtual sites 66: 66: Total mass 472.547 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 4 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 66 atoms 4 residues 66: 66: Including chain 3 in system: 61 atoms 3 residues 66: 66: Including chain 4 in system: 83 atoms 5 residues 66: 66: Now there are 261 atoms and 16 residues 66: 66: Total mass in system 1900.162 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (16 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 652 pairs 66: Before cleaning: 662 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 256, now 256 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 12 cmap torsion pairs 66: 66: There are 662 dihedrals, 47 impropers, 460 angles 66: 649 pairs, 256 bonds and 0 virtual sites 66: 66: Total mass 1864.131 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (16 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 14 donors and 15 acceptors were found. 66: There are 20 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 441 pairs 66: Before cleaning: 446 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 11 86 66: 66: 2 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (86 atoms, 11 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 11 residues with 172 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 173, now 173 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 9 cmap torsion pairs 66: 66: There are 446 dihedrals, 29 impropers, 312 angles 66: 438 pairs, 173 bonds and 0 virtual sites 66: 66: Total mass 1262.488 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 172 atoms 11 residues 66: 66: Including chain 2 in system: 83 atoms 5 residues 66: 66: Now there are 255 atoms and 16 residues 66: 66: Total mass in system 1864.131 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (14 ms) 66: [----------] 8 tests from ChainSep/Pdb2gmxTest (129 ms total) 66: 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (11 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (11 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (11 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (11 ms) 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest (45 ms total) 66: 66: [----------] 4 tests from Cyclic/Pdb2gmxTest 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: Moved all the water blocks to the end 66: 66: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 71 1527 66: 66: 2 'Q' 71 1527 66: 66: 3 'Q' 7 7 66: 66: 4 ' ' 10 10 (only water) 66: 66: 5 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'Q' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'Q' (7 atoms, 7 residues) 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 7 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: No bonds 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 0 angles 66: 0 pairs, 0 bonds and 0 virtual sites 66: 66: Total mass 170.135 a.m.u. 66: 66: Total charge 14.000 e 66: 66: Writing topology 66: 66: Processing chain 4 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 5 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain m9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: olecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 2297 atoms 71 residues 66: 66: Including chain 2 in system: 2297 atoms 71 residues 66: 66: Including chain 3 in system: 7 atoms 7 residues 66: 66: Including chain 4 in system: 30 atoms 10 residues 66: 66: Including chain 5 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.562 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (206 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (39 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 12080 pairs 66: Before cleaning: 13210 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Moved all the water blocks to the end 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 149 3061 66: 66: 2 ' ' 10 10 (only water) 66: 66: 3 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (3061 atoms, 149 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 149 residues with 4601 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4962, now 4962 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 13210 dihedrals, 366 impropers, 8868 angles 66: 11654 pairs, 4962 bonds and 0 virtual sites 66: 66: Total mass 46139.162 a.m.u. 66: 66: Total charge -128.000 e 66: 66: Writing topology 66: 66: Processing chain 2 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 3 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 4601 atoms 149 residues 66: 66: Including chain 2 in system: 30 atoms 10 residues 66: 66: Including chain 3 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.562 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (216 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (38 ms) 66: [----------] 4 tests from Cyclic/Pdb2gmxTest (501 ms total) 66: 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 5 47 66: 66: 2 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2325 dihedrals, 141 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.100 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 86 atoms 5 residues 66: 66: Including chain 2 in system: 878 atoms 60 residues 66: 66: Now there are 964 atoms and 65 residues 66: 66: Total mass in system 6519.802 a.m.u. 66: 66: Total charge in system 4.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file (46 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 188 pairs 66: Before cleaning: 198 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 3 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 4 38 66: 66: 2 'E' 5 47 66: 66: 3 'F' 5 47 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (38 atoms, 4 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 72 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 75, now 74 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 198 dihedrals, 18 impropers, 132 angles 66: 185 pairs, 74 bonds and 0 virtual sites 66: 66: Total mass 543.584 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'E' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'F' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 72 atoms 4 residues 66: 66: Including chain 2 in system: 86 atoms 5 residues 66: 66: Including chain 3 in system: 86 atoms 5 residues 66: 66: Now there are 244 atoms and 14 residues 66: 66: Total mass in system 1850.988 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file (19 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 2558 pairs 66: Before cleaning: 2568 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 65 460 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (460 atoms, 65 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 65 residues with 964 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 969, now 969 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2568 dihedrals, 164 impropers, 1773 angles 66: 2549 pairs, 969 bonds and 0 virtual sites 66: 66: Total mass 6519.802 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file (42 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 654 pairs 66: Before cleaning: 684 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 14 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (132 atoms, 14 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 14 residues with 244 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 253, now 252 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 684 dihedrals, 64 impropers, 450 angles 66: 645 pairs, 252 bonds and 0 virtual sites 66: 66: Total mass 1850.988 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file (18 ms) 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest (126 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 55 tests from 9 test suites ran. (1507 ms total) 66: [ PASSED ] 55 tests. 66/104 Test #66: Pdb2gmx3Test .............................. Passed 1.52 sec test 67 Start 67: CorrelationsTest 67: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/CorrelationsTest.xml" 67: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/correlationfunctions/tests 67: Test timeout computed to be: 30 67: [==========] Running 21 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 10 tests from AutocorrTest 67: [ RUN ] AutocorrTest.EacNormal 67: [ OK ] AutocorrTest.EacNormal (19 ms) 67: [ RUN ] AutocorrTest.EacNoNormalize 67: [ OK ] AutocorrTest.EacNoNormalize (10 ms) 67: [ RUN ] AutocorrTest.EacCos 67: [ OK ] AutocorrTest.EacCos (18 ms) 67: [ RUN ] AutocorrTest.EacVector 67: [ OK ] AutocorrTest.EacVector (29 ms) 67: [ RUN ] AutocorrTest.EacRcross 67: [ OK ] AutocorrTest.EacRcross (0 ms) 67: [ RUN ] AutocorrTest.EacP0 67: [ OK ] AutocorrTest.EacP0 (31 ms) 67: [ RUN ] AutocorrTest.EacP1 67: [ OK ] AutocorrTest.EacP1 (30 ms) 67: [ RUN ] AutocorrTest.EacP2 67: [ OK ] AutocorrTest.EacP2 (60 ms) 67: [ RUN ] AutocorrTest.EacP3 67: [ OK ] AutocorrTest.EacP3 (2 ms) 67: [ RUN ] AutocorrTest.EacP4 67: [ OK ] AutocorrTest.EacP4 (30 ms) 67: [----------] 10 tests from AutocorrTest (234 ms total) 67: 67: [----------] 10 tests from ExpfitTest 67: [ RUN ] ExpfitTest.EffnEXP1 67: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 67: [ RUN ] ExpfitTest.EffnEXP2 67: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 67: [ RUN ] ExpfitTest.EffnEXPEXP 67: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 67: [ RUN ] ExpfitTest.EffnEXP5 67: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP7 67: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP9 67: [ OK ] ExpfitTest.EffnEXP9 (7 ms) 67: [ RUN ] ExpfitTest.EffnERF 67: [ OK ] ExpfitTest.EffnERF (0 ms) 67: [ RUN ] ExpfitTest.EffnERREST 67: [ OK ] ExpfitTest.EffnERREST (1 ms) 67: [ RUN ] ExpfitTest.EffnVAC 67: [ OK ] ExpfitTest.EffnVAC (3 ms) 67: [ RUN ] ExpfitTest.EffnPRES 67: [ OK ] ExpfitTest.EffnPRES (6 ms) 67: [----------] 10 tests from ExpfitTest (24 ms total) 67: 67: [----------] 1 test from ManyAutocorrelationTest 67: [ RUN ] ManyAutocorrelationTest.Empty 67: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 67: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 21 tests from 3 test suites ran. (262 ms total) 67: [ PASSED ] 21 tests. 67/104 Test #67: CorrelationsTest .......................... Passed 0.27 sec test 68 Start 68: AnalysisDataUnitTests 68: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/analysisdata/tests 68: Test timeout computed to be: 30 68: [==========] Running 69 tests from 14 test suites. 68: [----------] Global test environment set-up. 68: [----------] 3 tests from AnalysisDataInitializationTest 68: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 68: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 68: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 68: 68: [----------] 4 tests from AnalysisArrayDataTest 68: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 68: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisArrayDataTest.StorageWorks 68: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 68: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 68: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 68: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 68: 68: [----------] 6 tests from AverageModuleTest 68: [ RUN ] AverageModuleTest.BasicTest 68: [ OK ] AverageModuleTest.BasicTest (0 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipointData 68: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 68: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 68: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeXAxis 68: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 68: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 68: [----------] 6 tests from AverageModuleTest (1 ms total) 68: 68: [----------] 2 tests from FrameAverageModuleTest 68: [ RUN ] FrameAverageModuleTest.BasicTest 68: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 68: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 68: 68: [----------] 7 tests from AnalysisHistogramSettingsTest 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 68: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 68: 68: [----------] 2 tests from SimpleHistogramModuleTest 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 68: 68: [----------] 3 tests from WeightedHistogramModuleTest 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 68: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 68: 68: [----------] 3 tests from BinAverageModuleTest 68: [ RUN ] BinAverageModuleTest.ComputesCorrectly 68: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 68: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from BinAverageModuleTest (0 ms total) 68: 68: [----------] 4 tests from AbstractAverageHistogramTest 68: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 68: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 68: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 68: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 68: 68: [----------] 3 tests from LifetimeModuleTest 68: [ RUN ] LifetimeModuleTest.BasicTest 68: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 68: [ RUN ] LifetimeModuleTest.CumulativeTest 68: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 68: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 68: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from LifetimeModuleTest (0 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 69 tests from 14 test suites ran. (13 ms total) 68: [ PASSED ] 69 tests. 68/104 Test #68: AnalysisDataUnitTests ..................... Passed 0.02 sec test 69 Start 69: CoordinateIOTests 69: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/CoordinateIOTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/coordinateio/tests 69: Test timeout computed to be: 30 69: [==========] Running 67 tests from 20 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from OutputSelectorDeathTest 69: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (2 ms) 69: [----------] 1 test from OutputSelectorDeathTest (2 ms total) 69: 69: [----------] 5 tests from TrajectoryFrameWriterTest 69: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 69: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 69: [----------] 5 tests from TrajectoryFrameWriterTest (5 ms total) 69: 69: [----------] 5 tests from OutputAdapterContainer 69: [ RUN ] OutputAdapterContainer.MakeEmpty 69: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 69: [ RUN ] OutputAdapterContainer.AddAdapter 69: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectBadAdapter 69: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 69: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 69: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 69: [----------] 5 tests from OutputAdapterContainer (0 ms total) 69: 69: [----------] 3 tests from RegisterFrameConverterTest 69: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 69: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 69: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 69: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 69: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 69: 69: [----------] 5 tests from FlagTest 69: [ RUN ] FlagTest.CanSetSimpleFlag 69: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 69: [ RUN ] FlagTest.CanAddNewBox 69: [ OK ] FlagTest.CanAddNewBox (0 ms) 69: [ RUN ] FlagTest.SetsImplicitPrecisionChange 69: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitStartTimeChange 69: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitTimeStepChange 69: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 69: [----------] 5 tests from FlagTest (0 ms total) 69: 69: [----------] 5 tests from SetAtomsTest 69: [ RUN ] SetAtomsTest.RemovesExistingAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 69: [ RUN ] SetAtomsTest.AddsNewAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 69: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (0 ms) 69: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 69: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 69: [----------] 5 tests from SetAtomsTest (4 ms total) 69: 69: [----------] 2 tests from SetBothTimeTest 69: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 69: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 69: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 69: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 69: [----------] 2 tests from SetBothTimeTest (0 ms total) 69: 69: [----------] 2 tests from SetStartTimeTest 69: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 69: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 69: [ RUN ] SetStartTimeTest.WorksWithZeroStart 69: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 69: [----------] 2 tests from SetStartTimeTest (0 ms total) 69: 69: [----------] 1 test from SetTimeStepTest 69: [ RUN ] SetTimeStepTest.SetTimeStepWorks 69: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 69: [----------] 1 test from SetTimeStepTest (0 ms total) 69: 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (6 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (3 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (2 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (1 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (8 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (2 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (2 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 67 tests from 20 test suites ran. (42 ms total) 69: [ PASSED ] 67 tests. 69/104 Test #69: CoordinateIOTests ......................... Passed 0.05 sec test 70 Start 70: TrajectoryAnalysisUnitTests 70: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests 70: Test timeout computed to be: 1920 70: [==========] Running 394 tests from 21 test suites. 70: [----------] Global test environment set-up. 70: [----------] 11 tests from AngleModuleTest 70: [ RUN ] AngleModuleTest.ComputesSimpleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesSimpleAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesDihedrals 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPairAngles (0 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (0 ms) 70: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system for different angles', 33 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesMultipleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesMultipleAngles (0 ms) 70: [ RUN ] AngleModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 70: [----------] 11 tests from AngleModuleTest (12 ms total) 70: 70: [----------] 5 tests from ClustsizeTest 70: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 2, cmax: 4, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 70: [ RUN ] ClustsizeTest.NoMolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 1, cmax: 6, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) 70: [ RUN ] ClustsizeTest.MolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 70: [ RUN ] ClustsizeTest.MolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 1, cmax: 6, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 70: [ RUN ] ClustsizeTest.MolCSize 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolCSize (1 ms) 70: [----------] 5 tests from ClustsizeTest (6 ms total) 70: 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (2 ms total) 70: 70: [----------] 4 tests from ConvertTrjModuleTest 70: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (4 ms) 70: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (4 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (0 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (0 ms) 70: [----------] 4 tests from ConvertTrjModuleTest (11 ms total) 70: 70: [----------] 6 tests from DistanceModuleTest 70: [ RUN ] DistanceModuleTest.ComputesDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 70: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 70: Number of samples: 4 70: Average distance: 1.81066 nm 70: Standard deviation: 0.79289 nm 70: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 70: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2 and res_cog x < 2.8: 70: Number of samples: 3 70: Average distance: 1.72076 nm 70: Standard deviation: 1.24839 nm 70: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: Contacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (2 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: SuccessiveContacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: ManyContacts: 70: Number of samples: 10 70: Average distance: 1.82913 nm 70: Standard deviation: 0.78478 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (2 ms) 70: [----------] 6 tests from DistanceModuleTest (13 ms total) 70: 70: [----------] 2 tests from ExtractClusterModuleTest 70: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 70: trr version: GMX_trn_file (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (1 ms) 70: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 70: [----------] 2 tests from ExtractClusterModuleTest (2 ms total) 70: 70: [----------] 2 tests from FreeVolumeModuleTest 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for 40 particles. These were set to zero. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 13 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.02 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 70: Fractional free volume 0.194 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (41 ms) 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 17 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.48 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 70: Fractional free volume 0.200 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (42 ms) 70: [----------] 2 tests from FreeVolumeModuleTest (84 ms total) 70: 70: [----------] 13 tests from MsdModuleTest 70: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 70: [ RUN ] MsdModuleTest.multipleGroupsWork 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to 1583333318 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.multipleGroupsWork (14 ms) 70: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.100 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 70: Analyzed 21 frames, last time 2.000 70: Setting the LD random seed to -515 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (13 ms) 70: [ RUN ] MsdModuleTest.trestartLessThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to 2126501871 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartLessThanDt (10 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -12595220 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDt (13 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to 1876931322 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (10 ms) 70: [ RUN ] MsdModuleTest.molTest 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -48475401 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.molTest (12 ms) 70: [ RUN ] MsdModuleTest.beginFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -520126489 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.beginFit (11 ms) 70: [ RUN ] MsdModuleTest.endFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -46144515 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.endFit (12 ms) 70: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: NOTE: You provided an index file 70: /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 70: (with -n), but it was not used by any selection. 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -108530309 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (12 ms) 70: [----------] 13 tests from MsdModuleTest (117 ms total) 70: 70: [----------] 9 tests from PairDistanceModuleTest 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (0 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 70: [----------] 9 tests from PairDistanceModuleTest (10 ms total) 70: 70: [----------] 5 tests from RdfModuleTest 70: [ RUN ] RdfModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.BasicTest (11 ms) 70: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 70: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (8 ms) 70: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (10 ms) 70: [ RUN ] RdfModuleTest.CalculatesSurf 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesSurf (4 ms) 70: [ RUN ] RdfModuleTest.CalculatesXY 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesXY (12 ms) 70: [----------] 5 tests from RdfModuleTest (47 ms total) 70: 70: [----------] 5 tests from SasaModuleTest 70: [ RUN ] SasaModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.BasicTest (5 ms) 70: [ RUN ] SasaModuleTest.HandlesSelectedResidues 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesSelectedResidues (2 ms) 70: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (3 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (3 ms) 70: [----------] 5 tests from SasaModuleTest (18 ms total) 70: 70: [----------] 9 tests from SelectModuleTest 70: [ RUN ] SelectModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.BasicTest (2 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 70: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 70: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 70: [ RUN ] SelectModuleTest.NormalizesSizes 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 70: [ RUN ] SelectModuleTest.WritesResidueNumbers 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueNumbers (0 ms) 70: [ RUN ] SelectModuleTest.WritesResidueIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueIndices (0 ms) 70: [ RUN ] SelectModuleTest.HandlesPrimeInAtomName 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.HandlesPrimeInAtomName (0 ms) 70: [----------] 9 tests from SelectModuleTest (11 ms total) 70: 70: [----------] 10 tests from SurfaceAreaTest 70: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 70: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 70: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 70: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints12 70: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints32 70: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints42 70: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints122 70: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 70: [ RUN ] SurfaceAreaTest.Computes100Points 70: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 70: [----------] 10 tests from SurfaceAreaTest (5 ms total) 70: 70: [----------] 4 tests from TopologyInformation 70: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 70: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 70: [ RUN ] TopologyInformation.WorksWithGroFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 70: [ RUN ] TopologyInformation.WorksWithPdbFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) 70: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file lysozyme.top, line 1465]: 70: System has non-zero total charge: 2.000000 70: Total charge should normally be an integer. See 70: https://manual.gromacs.org/current/user-guide/floating-point.html 70: for discussion on how close it should be to an integer. 70: 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 465.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 70: Setting the LD random seed to -1146159129 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 70: Analysing residue names: 70: There are: 10 Protein residues 70: Analysing Protein... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (227 ms) 70: [----------] 4 tests from TopologyInformation (229 ms total) 70: 70: [----------] 4 tests from TrajectoryModuleTest 70: [ RUN ] TrajectoryModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 70: [ RUN ] TrajectoryModuleTest.PlotsXOnly 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (0 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoForces 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 70: [----------] 4 tests from TrajectoryModuleTest (4 ms total) 70: 70: [----------] 5 tests from UnionFinderTest 70: [ RUN ] UnionFinderTest.WorksEmpty 70: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 70: [ RUN ] UnionFinderTest.BasicMerges 70: [ OK ] UnionFinderTest.BasicMerges (0 ms) 70: [ RUN ] UnionFinderTest.LargerMerges 70: [ OK ] UnionFinderTest.LargerMerges (0 ms) 70: [ RUN ] UnionFinderTest.LongRightMerge 70: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 70: [ RUN ] UnionFinderTest.LongLeftMerge 70: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 70: [----------] 5 tests from UnionFinderTest (0 ms total) 70: 70: [----------] 1 test from MappedUnionFinderTest 70: [ RUN ] MappedUnionFinderTest.BasicMerges 70: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 70: [----------] 1 test from MappedUnionFinderTest (0 ms total) 70: 70: [----------] 192 tests from MoleculeTests/DsspModuleTest 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (8 ms) 70: [----------] 192 tests from MoleculeTests/DsspModuleTest (2086 ms total) 70: 70: [----------] 3 tests from GyrateTests/GyrateModuleTest 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (3 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (3 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (3 ms) 70: [----------] 3 tests from GyrateTests/GyrateModuleTest (11 ms total) 70: 70: [----------] 96 tests from HBondTests/HbondModuleTest 70: [ RUN ] HBondTests/HbondModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/0 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/1 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/2 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/3 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/3 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/4 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/4 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/5 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/5 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/6 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/6 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/7 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/7 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/8 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/8 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/9 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/9 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/10 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/10 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/11 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/11 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/12 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/12 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/13 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/13 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/14 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/14 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/15 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/15 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/16 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/16 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/17 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/17 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/18 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/18 (7 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/19 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/19 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/20 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/20 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/21 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/21 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/22 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/22 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/23 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/23 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/24 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/24 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/25 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/25 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/26 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/26 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/27 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/27 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/28 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/28 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/29 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/29 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/30 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/30 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/31 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/31 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/32 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/32 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/33 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/33 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/34 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/34 (28 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/35 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/35 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/36 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/36 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/37 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/37 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/38 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/38 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/39 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/39 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/40 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/40 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/41 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/41 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/42 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/42 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/43 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/43 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/44 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/44 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/45 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/45 (36 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/46 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/46 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/47 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/47 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/48 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/48 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/49 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/49 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/50 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/50 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/51 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/51 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/52 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/52 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/53 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/53 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/54 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/54 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/55 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/55 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/56 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/56 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/57 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/57 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/58 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/58 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/59 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/59 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/60 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/60 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/61 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/61 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/62 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/62 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/63 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/63 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/64 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/64 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/65 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/65 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/66 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/66 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/67 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/67 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/68 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/68 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/69 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/69 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/70 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/70 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/71 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/71 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/72 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/72 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/73 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/73 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/74 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/74 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/75 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/75 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/76 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/76 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/77 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/77 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/78 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/78 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/79 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/79 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/80 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/80 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/81 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/81 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/82 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/82 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/83 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/83 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/84 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/84 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/85 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/85 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/86 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/86 (38 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/87 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/87 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/88 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/88 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/89 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/89 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/90 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/90 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/91 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/91 (36 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/92 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/92 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/93 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/93 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/94 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/94 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/95 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/95 (32 ms) 70: [----------] 96 tests from HBondTests/HbondModuleTest (2517 ms total) 70: 70: [----------] 4 tests from MoleculeTests/ScatteringModule 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (5 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (161 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (4 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (37 ms) 70: [----------] 4 tests from MoleculeTests/ScatteringModule (210 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 394 tests from 21 test suites ran. (5404 ms total) 70: [ PASSED ] 394 tests. 70/104 Test #70: TrajectoryAnalysisUnitTests ............... Passed 5.42 sec test 71 Start 71: EnergyAnalysisUnitTests 71: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests 71: Test timeout computed to be: 30 71: [==========] Running 12 tests from 5 test suites. 71: [----------] Global test environment set-up. 71: [----------] 2 tests from EnergyTermTest 71: [ RUN ] EnergyTermTest.ConstructWorks 71: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 71: [ RUN ] EnergyTermTest.AddFrameWorks 71: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 71: [----------] 2 tests from EnergyTermTest (0 ms total) 71: 71: [----------] 1 test from DhdlTest 71: [ RUN ] DhdlTest.ExtractDhdl 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 71: Note: file tpx version 110, software tpx version 138 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 71: 71: 71: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 71: [ OK ] DhdlTest.ExtractDhdl (4 ms) 71: [----------] 1 test from DhdlTest (4 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.ExtractOrires 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 71: Note: file tpx version 111, software tpx version 138 71: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 71: End your selection with 0 71: Selecting all 7 orientation restraints 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 71: [ OK ] OriresTest.ExtractOrires (4 ms) 71: [----------] 1 test from OriresTest (4 ms total) 71: 71: [----------] 5 tests from EnergyTest 71: [ RUN ] EnergyTest.ExtractEnergy 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: [ OK ] EnergyTest.ExtractEnergy (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyByNumber 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Pres. DC -268.49 3 8.52175 13.2804 (bar) 71: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyMixed 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 71: [----------] 5 tests from EnergyTest (5 ms total) 71: 71: [----------] 3 tests from ViscosityTest 71: [ RUN ] ViscosityTest.EinsteinViscosity 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosity (28 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityIntegral (23 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (23 ms) 71: [----------] 3 tests from ViscosityTest (75 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 5 test suites ran. (89 ms total) 71: [ PASSED ] 12 tests. 71/104 Test #71: EnergyAnalysisUnitTests ................... Passed 0.10 sec test 72 Start 72: ToolUnitTests 72: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/ToolUnitTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests 72: Test timeout computed to be: 1920 72: [==========] Running 70 tests from 8 test suites. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from DumpTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -75923473 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] DumpTest.WorksWithTpr 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 72: inputrec: 72: integrator = md 72: tinit = 0 72: dt = 0.001 72: nsteps = 0 72: init-step = 0 72: simulation-part = 1 72: mts = false 72: mass-repartition-factor = 1 72: comm-mode = Linear 72: nstcomm = 100 72: bd-fric = 0 72: ld-seed = -75923473 72: emtol = 10 72: emstep = 0.01 72: niter = 20 72: fcstep = 0 72: nstcgsteep = 1000 72: nbfgscorr = 10 72: rtpi = 0.05 72: nstxout = 0 72: nstvout = 0 72: nstfout = 0 72: nstlog = 1000 72: nstcalcenergy = 100 72: nstenergy = 1000 72: nstxout-compressed = 0 72: compressed-x-precision = 1000 72: cutoff-scheme = Verlet 72: nstlist = 10 72: pbc = xyz 72: periodic-molecules = false 72: verlet-buffer-tolerance = -1 72: verlet-buffer-pressure-tolerance = 0.5 72: rlist = 1.1 72: coulombtype = Cut-off 72: coulomb-modifier = Potential-shift 72: rcoulomb-switch = 0 72: rcoulomb = 1 72: epsilon-r = 1 72: epsilon-rf = inf 72: vdw-type = Cut-off 72: vdw-modifier = Potential-shift 72: rvdw-switch = 0 72: rvdw = 1 72: DispCorr = No 72: table-extension = 1 72: fourierspacing = 0.12 72: fourier-nx = 0 72: fourier-ny = 0 72: fourier-nz = 0 72: pme-order = 4 72: ewald-rtol = 1e-05 72: ewald-rtol-lj = 0.001 72: lj-pme-comb-rule = Geometric 72: ewald-geometry = 3d 72: epsilon-surface = 0 72: ensemble-temperature-setting = not available 72: tcoupl = No 72: nsttcouple = -1 72: nh-chain-length = 0 72: print-nose-hoover-chain-variables = false 72: pcoupl = No 72: refcoord-scaling = No 72: posres-com: not available 72: posres-comB: not available 72: QMMM = false 72: qm-opts: 72: ngQM = 0 72: constraint-algorithm = Lincs 72: continuation = false 72: Shake-SOR = false 72: shake-tol = 0.0001 72: lincs-order = 4 72: lincs-iter = 1 72: lincs-warnangle = 30 72: nwall = 0 72: wall-type = 9-3 72: wall-r-linpot = -1 72: wall-atomtype[0] = -1 72: wall-atomtype[1] = -1 72: wall-density[0] = 0 72: wall-density[1] = 0 72: wall-ewald-zfac = 3 72: pull = false 72: awh = false 72: rotation = false 72: interactiveMD = false 72: disre = No 72: disre-weighting = Conservative 72: disre-mixed = false 72: dr-fc = 1000 72: dr-tau = 0 72: nstdisreout = 100 72: orire-fc = 0 72: orire-tau = 0 72: nstorireout = 100 72: free-energy = no 72: cos-acceleration = 0 72: deform (3x3): 72: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: simulated-tempering = false 72: swapcoords = no 72: userint1 = 0 72: userint2 = 0 72: userint3 = 0 72: userint4 = 0 72: userreal1 = 0 72: userreal2 = 0 72: userreal3 = 0 72: userreal4 = 0 72: applied-forces: 72: electric-field: 72: x: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: y: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: z: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: density-guided-simulation: 72: active = false 72: group = protein 72: similarity-measure = inner-product 72: atom-spreading-weight = unity 72: force-constant = 1e+09 72: gaussian-transform-spreading-width = 0.2 72: gaussian-transform-spreading-range-in-multiples-of-width = 4 72: reference-density-filename = reference.mrc 72: nst = 1 72: normalize-densities = true 72: adaptive-force-scaling = false 72: adaptive-force-scaling-time-constant = 4 72: shift-vector = 72: transformation-matrix = 72: qmmm-cp2k: 72: active = false 72: qmgroup = System 72: qmmethod = PBE 72: qmfilenames = 72: qmcharge = 0 72: qmmultiplicity = 1 72: colvars: 72: active = false 72: configfile = 72: seed = -1 72: nnpot: 72: active = false 72: modelfile = model.pt 72: input-group = System 72: link-type = H 72: link-distance = 0.1 72: pair-cutoff = 0 72: embedding = mechanical 72: nnp-charge = 0 72: model-input1 = 72: model-input2 = 72: model-input3 = 72: model-input4 = 72: model-input5 = 72: model-input6 = 72: model-input7 = 72: model-input8 = 72: model-input9 = 72: fast-multipole-method: 72: fmm: 72: backend = inactive 72: exafmm-order = 6 72: exafmm-direct-range = 2 72: exafmm-direct-provider = GROMACS 72: exafmm-tree-type = uniform 72: exafmm-tree-depth = 0 72: exafmm-max-particles-per-cell = 0 72: fmsolvr-order = 8 72: fmsolvr-direct-range = 1 72: fmsolvr-direct-provider = FMM 72: fmsolvr-dipole-compensation = true 72: fmsolvr-tree-depth = 3 72: fmsolvr-sparse = false 72: grpopts: 72: nrdf: 465 72: ref-t: 0 72: tau-t: 0 72: annealing: No 72: annealing-npoints: 0 72: acc: 0 0 0 72: nfreeze: N N N 72: energygrp-flags[ 0]: 0 72: header: 72: bIr = present 72: bBox = present 72: bTop = present 72: bX = present 72: bV = present 72: bF = not present 72: natoms = 156 72: lambda = 0.000000e+00 72: buffer size = 47154 72: topology: 72: name="First 10 residues from 1AKI" 72: #atoms = 156 72: #molblock = 1 72: molblock (0): 72: moltype = 0 "Protein_chain_B" 72: #molecules = 1 72: #posres_xA = 0 72: #posres_xB = 0 72: bIntermolecularInteractions = false 72: ffparams: 72: atnr=10 72: ntypes=212 72: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 72: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 72: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 72: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 72: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 72: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 72: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 72: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 72: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 72: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 72: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 72: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 72: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 72: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 72: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 72: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 72: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 72: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 72: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 72: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 72: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 72: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 72: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 72: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 72: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 72: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 72: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 72: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 72: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 72: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 72: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 72: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 72: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 72: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 72: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 72: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 72: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 72: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 72: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 72: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 72: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 72: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 72: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 72: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 72: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 72: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 72: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 72: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 72: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 72: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 72: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 72: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 72: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 72: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 72: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 72: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 72: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 72: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 72: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 72: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 72: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 72: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 72: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 72: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 72: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 72: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 72: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 72: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 72: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 72: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 72: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 72: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 72: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 72: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 72: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 72: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 72: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 72: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 72: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 72: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 72: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 72: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 72: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 72: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 72: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 72: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 72: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 72: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 72: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 72: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 72: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 72: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 72: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 72: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 72: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 72: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 72: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 72: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 72: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 72: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 72: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 72: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 72: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 72: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 72: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 72: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 72: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 72: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 72: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 72: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 72: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 72: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 72: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 72: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 72: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 72: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 72: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 72: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 72: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 72: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 72: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 72: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 72: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 72: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 72: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 72: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 72: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 72: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 72: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 72: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 72: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 72: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 72: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 72: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 72: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 72: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 72: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 72: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 72: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 72: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 72: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 72: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 72: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 72: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 72: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 72: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 72: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 72: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 72: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 72: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 72: reppow = 12 72: fudgeQQ = 0.5 72: cmap 72: moltype (0): 72: name="Protein_chain_B" 72: atoms: 72: atom (156): 72: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 72: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 72: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 72: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 72: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 72: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 72: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 72: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 72: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 72: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 72: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 72: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 72: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 72: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 72: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 72: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 72: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 72: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 72: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 72: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 72: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 72: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 72: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 72: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 72: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 72: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 72: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 72: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 72: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 72: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 72: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 72: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 72: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 72: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 72: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 72: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 72: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 72: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 72: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 72: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 72: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 72: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 72: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 72: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 72: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 72: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 72: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 72: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 72: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 72: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 72: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 72: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 72: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 72: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 72: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 72: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 72: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 72: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 72: atom (156): 72: atom[0]={name="N"} 72: atom[1]={name="H1"} 72: atom[2]={name="H2"} 72: atom[3]={name="H3"} 72: atom[4]={name="CA"} 72: atom[5]={name="HA"} 72: atom[6]={name="CB"} 72: atom[7]={name="HB1"} 72: atom[8]={name="HB2"} 72: atom[9]={name="CG"} 72: atom[10]={name="HG1"} 72: atom[11]={name="HG2"} 72: atom[12]={name="CD"} 72: atom[13]={name="HD1"} 72: atom[14]={name="HD2"} 72: atom[15]={name="CE"} 72: atom[16]={name="HE1"} 72: atom[17]={name="HE2"} 72: atom[18]={name="NZ"} 72: atom[19]={name="HZ1"} 72: atom[20]={name="HZ2"} 72: atom[21]={name="HZ3"} 72: atom[22]={name="C"} 72: atom[23]={name="O"} 72: atom[24]={name="N"} 72: atom[25]={name="H"} 72: atom[26]={name="CA"} 72: atom[27]={name="HA"} 72: atom[28]={name="CB"} 72: atom[29]={name="HB"} 72: atom[30]={name="CG1"} 72: atom[31]={name="HG11"} 72: atom[32]={name="HG12"} 72: atom[33]={name="HG13"} 72: atom[34]={name="CG2"} 72: atom[35]={name="HG21"} 72: atom[36]={name="HG22"} 72: atom[37]={name="HG23"} 72: atom[38]={name="C"} 72: atom[39]={name="O"} 72: atom[40]={name="N"} 72: atom[41]={name="H"} 72: atom[42]={name="CA"} 72: atom[43]={name="HA"} 72: atom[44]={name="CB"} 72: atom[45]={name="HB1"} 72: atom[46]={name="HB2"} 72: atom[47]={name="CG"} 72: atom[48]={name="CD1"} 72: atom[49]={name="HD1"} 72: atom[50]={name="CD2"} 72: atom[51]={name="HD2"} 72: atom[52]={name="CE1"} 72: atom[53]={name="HE1"} 72: atom[54]={name="CE2"} 72: atom[55]={name="HE2"} 72: atom[56]={name="CZ"} 72: atom[57]={name="HZ"} 72: atom[58]={name="C"} 72: atom[59]={name="O"} 72: atom[60]={name="N"} 72: atom[61]={name="H"} 72: atom[62]={name="CA"} 72: atom[63]={name="HA1"} 72: atom[64]={name="HA2"} 72: atom[65]={name="C"} 72: atom[66]={name="O"} 72: atom[67]={name="N"} 72: atom[68]={name="H"} 72: atom[69]={name="CA"} 72: atom[70]={name="HA"} 72: atom[71]={name="CB"} 72: atom[72]={name="HB1"} 72: atom[73]={name="HB2"} 72: atom[74]={name="CG"} 72: atom[75]={name="HG1"} 72: atom[76]={name="HG2"} 72: atom[77]={name="CD"} 72: atom[78]={name="HD1"} 72: atom[79]={name="HD2"} 72: atom[80]={name="NE"} 72: atom[81]={name="HE"} 72: atom[82]={name="CZ"} 72: atom[83]={name="NH1"} 72: atom[84]={name="HH11"} 72: atom[85]={name="HH12"} 72: atom[86]={name="NH2"} 72: atom[87]={name="HH21"} 72: atom[88]={name="HH22"} 72: atom[89]={name="C"} 72: atom[90]={name="O"} 72: atom[91]={name="N"} 72: atom[92]={name="H"} 72: atom[93]={name="CA"} 72: atom[94]={name="HA"} 72: atom[95]={name="CB"} 72: atom[96]={name="HB1"} 72: atom[97]={name="HB2"} 72: atom[98]={name="SG"} 72: atom[99]={name="HG"} 72: atom[100]={name="C"} 72: atom[101]={name="O"} 72: atom[102]={name="N"} 72: atom[103]={name="H"} 72: atom[104]={name="CA"} 72: atom[105]={name="HA"} 72: atom[106]={name="CB"} 72: atom[107]={name="HB1"} 72: atom[108]={name="HB2"} 72: atom[109]={name="CG"} 72: atom[110]={name="HG1"} 72: atom[111]={name="HG2"} 72: atom[112]={name="CD"} 72: atom[113]={name="OE1"} 72: atom[114]={name="OE2"} 72: atom[115]={name="C"} 72: atom[116]={name="O"} 72: atom[117]={name="N"} 72: atom[118]={name="H"} 72: atom[119]={name="CA"} 72: atom[120]={name="HA"} 72: atom[121]={name="CB"} 72: atom[122]={name="HB1"} 72: atom[123]={name="HB2"} 72: atom[124]={name="CG"} 72: atom[125]={name="HG"} 72: atom[126]={name="CD1"} 72: atom[127]={name="HD11"} 72: atom[128]={name="HD12"} 72: atom[129]={name="HD13"} 72: atom[130]={name="CD2"} 72: atom[131]={name="HD21"} 72: atom[132]={name="HD22"} 72: atom[133]={name="HD23"} 72: atom[134]={name="C"} 72: atom[135]={name="O"} 72: atom[136]={name="N"} 72: atom[137]={name="H"} 72: atom[138]={name="CA"} 72: atom[139]={name="HA"} 72: atom[140]={name="CB"} 72: atom[141]={name="HB1"} 72: atom[142]={name="HB2"} 72: atom[143]={name="HB3"} 72: atom[144]={name="C"} 72: atom[145]={name="O"} 72: atom[146]={name="N"} 72: atom[147]={name="H"} 72: atom[148]={name="CA"} 72: atom[149]={name="HA"} 72: atom[150]={name="CB"} 72: atom[151]={name="HB1"} 72: atom[152]={name="HB2"} 72: atom[153]={name="HB3"} 72: atom[154]={name="C"} 72: atom[155]={name="O"} 72: type (156): 72: type[0]={name="opls_287",nameB="opls_287"} 72: type[1]={name="opls_290",nameB="opls_290"} 72: type[2]={name="opls_290",nameB="opls_290"} 72: type[3]={name="opls_290",nameB="opls_290"} 72: type[4]={name="opls_293B",nameB="opls_293B"} 72: type[5]={name="opls_140",nameB="opls_140"} 72: type[6]={name="opls_136",nameB="opls_136"} 72: type[7]={name="opls_140",nameB="opls_140"} 72: type[8]={name="opls_140",nameB="opls_140"} 72: type[9]={name="opls_136",nameB="opls_136"} 72: type[10]={name="opls_140",nameB="opls_140"} 72: type[11]={name="opls_140",nameB="opls_140"} 72: type[12]={name="opls_136",nameB="opls_136"} 72: type[13]={name="opls_140",nameB="opls_140"} 72: type[14]={name="opls_140",nameB="opls_140"} 72: type[15]={name="opls_292",nameB="opls_292"} 72: type[16]={name="opls_140",nameB="opls_140"} 72: type[17]={name="opls_140",nameB="opls_140"} 72: type[18]={name="opls_287",nameB="opls_287"} 72: type[19]={name="opls_290",nameB="opls_290"} 72: type[20]={name="opls_290",nameB="opls_290"} 72: type[21]={name="opls_290",nameB="opls_290"} 72: type[22]={name="opls_235",nameB="opls_235"} 72: type[23]={name="opls_236",nameB="opls_236"} 72: type[24]={name="opls_238",nameB="opls_238"} 72: type[25]={name="opls_241",nameB="opls_241"} 72: type[26]={name="opls_224B",nameB="opls_224B"} 72: type[27]={name="opls_140",nameB="opls_140"} 72: type[28]={name="opls_137",nameB="opls_137"} 72: type[29]={name="opls_140",nameB="opls_140"} 72: type[30]={name="opls_135",nameB="opls_135"} 72: type[31]={name="opls_140",nameB="opls_140"} 72: type[32]={name="opls_140",nameB="opls_140"} 72: type[33]={name="opls_140",nameB="opls_140"} 72: type[34]={name="opls_135",nameB="opls_135"} 72: type[35]={name="opls_140",nameB="opls_140"} 72: type[36]={name="opls_140",nameB="opls_140"} 72: type[37]={name="opls_140",nameB="opls_140"} 72: type[38]={name="opls_235",nameB="opls_235"} 72: type[39]={name="opls_236",nameB="opls_236"} 72: type[40]={name="opls_238",nameB="opls_238"} 72: type[41]={name="opls_241",nameB="opls_241"} 72: type[42]={name="opls_224B",nameB="opls_224B"} 72: type[43]={name="opls_140",nameB="opls_140"} 72: type[44]={name="opls_149",nameB="opls_149"} 72: type[45]={name="opls_140",nameB="opls_140"} 72: type[46]={name="opls_140",nameB="opls_140"} 72: type[47]={name="opls_145",nameB="opls_145"} 72: type[48]={name="opls_145",nameB="opls_145"} 72: type[49]={name="opls_146",nameB="opls_146"} 72: type[50]={name="opls_145",nameB="opls_145"} 72: type[51]={name="opls_146",nameB="opls_146"} 72: type[52]={name="opls_145",nameB="opls_145"} 72: type[53]={name="opls_146",nameB="opls_146"} 72: type[54]={name="opls_145",nameB="opls_145"} 72: type[55]={name="opls_146",nameB="opls_146"} 72: type[56]={name="opls_145",nameB="opls_145"} 72: type[57]={name="opls_146",nameB="opls_146"} 72: type[58]={name="opls_235",nameB="opls_235"} 72: type[59]={name="opls_236",nameB="opls_236"} 72: type[60]={name="opls_238",nameB="opls_238"} 72: type[61]={name="opls_241",nameB="opls_241"} 72: type[62]={name="opls_223B",nameB="opls_223B"} 72: type[63]={name="opls_140",nameB="opls_140"} 72: type[64]={name="opls_140",nameB="opls_140"} 72: type[65]={name="opls_235",nameB="opls_235"} 72: type[66]={name="opls_236",nameB="opls_236"} 72: type[67]={name="opls_238",nameB="opls_238"} 72: type[68]={name="opls_241",nameB="opls_241"} 72: type[69]={name="opls_224B",nameB="opls_224B"} 72: type[70]={name="opls_140",nameB="opls_140"} 72: type[71]={name="opls_136",nameB="opls_136"} 72: type[72]={name="opls_140",nameB="opls_140"} 72: type[73]={name="opls_140",nameB="opls_140"} 72: type[74]={name="opls_308",nameB="opls_308"} 72: type[75]={name="opls_140",nameB="opls_140"} 72: type[76]={name="opls_140",nameB="opls_140"} 72: type[77]={name="opls_307",nameB="opls_307"} 72: type[78]={name="opls_140",nameB="opls_140"} 72: type[79]={name="opls_140",nameB="opls_140"} 72: type[80]={name="opls_303",nameB="opls_303"} 72: type[81]={name="opls_304",nameB="opls_304"} 72: type[82]={name="opls_302",nameB="opls_302"} 72: type[83]={name="opls_300",nameB="opls_300"} 72: type[84]={name="opls_301",nameB="opls_301"} 72: type[85]={name="opls_301",nameB="opls_301"} 72: type[86]={name="opls_300",nameB="opls_300"} 72: type[87]={name="opls_301",nameB="opls_301"} 72: type[88]={name="opls_301",nameB="opls_301"} 72: type[89]={name="opls_235",nameB="opls_235"} 72: type[90]={name="opls_236",nameB="opls_236"} 72: type[91]={name="opls_238",nameB="opls_238"} 72: type[92]={name="opls_241",nameB="opls_241"} 72: type[93]={name="opls_224B",nameB="opls_224B"} 72: type[94]={name="opls_140",nameB="opls_140"} 72: type[95]={name="opls_206",nameB="opls_206"} 72: type[96]={name="opls_140",nameB="opls_140"} 72: type[97]={name="opls_140",nameB="opls_140"} 72: type[98]={name="opls_200",nameB="opls_200"} 72: type[99]={name="opls_204",nameB="opls_204"} 72: type[100]={name="opls_235",nameB="opls_235"} 72: type[101]={name="opls_236",nameB="opls_236"} 72: type[102]={name="opls_238",nameB="opls_238"} 72: type[103]={name="opls_241",nameB="opls_241"} 72: type[104]={name="opls_224B",nameB="opls_224B"} 72: type[105]={name="opls_140",nameB="opls_140"} 72: type[106]={name="opls_136",nameB="opls_136"} 72: type[107]={name="opls_140",nameB="opls_140"} 72: type[108]={name="opls_140",nameB="opls_140"} 72: type[109]={name="opls_274",nameB="opls_274"} 72: type[110]={name="opls_140",nameB="opls_140"} 72: type[111]={name="opls_140",nameB="opls_140"} 72: type[112]={name="opls_271",nameB="opls_271"} 72: type[113]={name="opls_272",nameB="opls_272"} 72: type[114]={name="opls_272",nameB="opls_272"} 72: type[115]={name="opls_235",nameB="opls_235"} 72: type[116]={name="opls_236",nameB="opls_236"} 72: type[117]={name="opls_238",nameB="opls_238"} 72: type[118]={name="opls_241",nameB="opls_241"} 72: type[119]={name="opls_224B",nameB="opls_224B"} 72: type[120]={name="opls_140",nameB="opls_140"} 72: type[121]={name="opls_136",nameB="opls_136"} 72: type[122]={name="opls_140",nameB="opls_140"} 72: type[123]={name="opls_140",nameB="opls_140"} 72: type[124]={name="opls_137",nameB="opls_137"} 72: type[125]={name="opls_140",nameB="opls_140"} 72: type[126]={name="opls_135",nameB="opls_135"} 72: type[127]={name="opls_140",nameB="opls_140"} 72: type[128]={name="opls_140",nameB="opls_140"} 72: type[129]={name="opls_140",nameB="opls_140"} 72: type[130]={name="opls_135",nameB="opls_135"} 72: type[131]={name="opls_140",nameB="opls_140"} 72: type[132]={name="opls_140",nameB="opls_140"} 72: type[133]={name="opls_140",nameB="opls_140"} 72: type[134]={name="opls_235",nameB="opls_235"} 72: type[135]={name="opls_236",nameB="opls_236"} 72: type[136]={name="opls_238",nameB="opls_238"} 72: type[137]={name="opls_241",nameB="opls_241"} 72: type[138]={name="opls_224B",nameB="opls_224B"} 72: type[139]={name="opls_140",nameB="opls_140"} 72: type[140]={name="opls_135",nameB="opls_135"} 72: type[141]={name="opls_140",nameB="opls_140"} 72: type[142]={name="opls_140",nameB="opls_140"} 72: type[143]={name="opls_140",nameB="opls_140"} 72: type[144]={name="opls_235",nameB="opls_235"} 72: type[145]={name="opls_236",nameB="opls_236"} 72: type[146]={name="opls_238",nameB="opls_238"} 72: type[147]={name="opls_241",nameB="opls_241"} 72: type[148]={name="opls_224B",nameB="opls_224B"} 72: type[149]={name="opls_140",nameB="opls_140"} 72: type[150]={name="opls_135",nameB="opls_135"} 72: type[151]={name="opls_140",nameB="opls_140"} 72: type[152]={name="opls_140",nameB="opls_140"} 72: type[153]={name="opls_140",nameB="opls_140"} 72: type[154]={name="opls_235",nameB="opls_235"} 72: type[155]={name="opls_236",nameB="opls_236"} 72: residue (10): 72: residue[0]={name="LYS", nr=1, ic=' '} 72: residue[1]={name="VAL", nr=2, ic=' '} 72: residue[2]={name="PHE", nr=3, ic=' '} 72: residue[3]={name="GLY", nr=4, ic=' '} 72: residue[4]={name="ARG", nr=5, ic=' '} 72: residue[5]={name="CYS", nr=6, ic=' '} 72: residue[6]={name="GLU", nr=7, ic=' '} 72: residue[7]={name="LEU", nr=8, ic=' '} 72: residue[8]={name="ALA", nr=9, ic=' '} 72: residue[9]={name="ALA", nr=10, ic=' '} 72: excls: 72: numLists=156 72: numElements=1828 72: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 72: 23, 24, 25, 26} 72: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 72: 14, 15, 22, 23, 24} 72: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 72: 16, 17, 18, 22} 72: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 72: 17, 18, 19, 20, 21} 72: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 72: 20, 21} 72: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 72: 26, 27, 28, 38} 72: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 72: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 72: 30, 34, 38, 39, 40} 72: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 72: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 72: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 72: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40} 72: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 72: 34, 35, 36, 37, 38, 39, 40} 72: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40, 41, 42, 43, 44, 58} 72: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 72: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 72: 45, 46, 47, 58, 59, 60} 72: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 72: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 72: 48, 50, 58, 59, 60, 61, 62} 72: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60} 72: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 72: 50, 51, 52, 54, 58, 59, 60} 72: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 72: 52, 53, 54, 55, 56, 58} 72: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 72: 54, 56, 57} 72: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 72: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 72: 55, 56, 57} 72: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 72: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 72: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 72: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 72: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 72: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60, 61, 62, 63, 64, 65} 72: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 72: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 72: 65, 66, 67} 72: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 72: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 72: 68, 69} 72: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72: 70, 71, 89} 72: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 72: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72: 72, 73, 74, 89, 90, 91} 72: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 72: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 72: 75, 76, 77, 89, 90, 91, 92, 93} 72: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91} 72: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 72: 77, 78, 79, 80, 89, 90, 91} 72: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 72: 79, 80, 81, 82, 89} 72: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 72: 81, 82, 83, 86} 72: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 72: 84, 85, 86, 87, 88} 72: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 72: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 72: 87, 88} 72: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[84][num=6]={80, 82, 83, 84, 85, 86} 72: excls[85][num=6]={80, 82, 83, 84, 85, 86} 72: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[87][num=6]={80, 82, 83, 86, 87, 88} 72: excls[88][num=6]={80, 82, 83, 86, 87, 88} 72: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91, 92, 93, 94, 95, 100} 72: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 72: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 72: 96, 97, 98, 100, 101, 102} 72: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 72: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 72: 99, 100, 101, 102, 103, 104} 72: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102} 72: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 72: 101, 102} 72: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[99][num=6]={93, 95, 96, 97, 98, 99} 72: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102, 103, 104, 105, 106, 115} 72: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 72: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 72: 106, 107, 108, 109, 115, 116, 117} 72: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 72: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 72: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 72: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117} 72: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 110, 111, 112, 113, 114, 115, 116, 117} 72: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 113, 114, 115} 72: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 72: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 72: 120, 121, 122, 123, 124, 134, 135, 136} 72: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 72: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 72: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136} 72: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 72: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 127, 128, 129, 130, 131, 132, 133, 134} 72: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 72: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 72: 139, 140, 141, 142, 143, 144, 145, 146} 72: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 72: 142, 143, 144, 145, 146, 147, 148} 72: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 72: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 72: 149, 150, 151, 152, 153, 154, 155} 72: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 72: 152, 153, 154, 155} 72: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[155][num=6]={146, 148, 149, 150, 154, 155} 72: Bond: 72: nr: 468 72: iatoms: 72: 0 type=100 (BONDS) 0 1 72: 1 type=100 (BONDS) 0 2 72: 2 type=100 (BONDS) 0 3 72: 3 type=101 (BONDS) 0 4 72: 4 type=102 (BONDS) 4 5 72: 5 type=103 (BONDS) 4 6 72: 6 type=104 (BONDS) 4 22 72: 7 type=102 (BONDS) 6 7 72: 8 type=102 (BONDS) 6 8 72: 9 type=103 (BONDS) 6 9 72: 10 type=102 (BONDS) 9 10 72: 11 type=102 (BONDS) 9 11 72: 12 type=103 (BONDS) 9 12 72: 13 type=102 (BONDS) 12 13 72: 14 type=102 (BONDS) 12 14 72: 15 type=103 (BONDS) 12 15 72: 16 type=102 (BONDS) 15 16 72: 17 type=102 (BONDS) 15 17 72: 18 type=101 (BONDS) 15 18 72: 19 type=100 (BONDS) 18 19 72: 20 type=100 (BONDS) 18 20 72: 21 type=100 (BONDS) 18 21 72: 22 type=105 (BONDS) 22 23 72: 23 type=106 (BONDS) 22 24 72: 24 type=100 (BONDS) 24 25 72: 25 type=107 (BONDS) 24 26 72: 26 type=102 (BONDS) 26 27 72: 27 type=103 (BONDS) 26 28 72: 28 type=104 (BONDS) 26 38 72: 29 type=102 (BONDS) 28 29 72: 30 type=103 (BONDS) 28 30 72: 31 type=103 (BONDS) 28 34 72: 32 type=102 (BONDS) 30 31 72: 33 type=102 (BONDS) 30 32 72: 34 type=102 (BONDS) 30 33 72: 35 type=102 (BONDS) 34 35 72: 36 type=102 (BONDS) 34 36 72: 37 type=102 (BONDS) 34 37 72: 38 type=105 (BONDS) 38 39 72: 39 type=106 (BONDS) 38 40 72: 40 type=100 (BONDS) 40 41 72: 41 type=107 (BONDS) 40 42 72: 42 type=102 (BONDS) 42 43 72: 43 type=103 (BONDS) 42 44 72: 44 type=104 (BONDS) 42 58 72: 45 type=102 (BONDS) 44 45 72: 46 type=102 (BONDS) 44 46 72: 47 type=108 (BONDS) 44 47 72: 48 type=109 (BONDS) 47 48 72: 49 type=109 (BONDS) 47 50 72: 50 type=110 (BONDS) 48 49 72: 51 type=109 (BONDS) 48 52 72: 52 type=110 (BONDS) 50 51 72: 53 type=109 (BONDS) 50 54 72: 54 type=110 (BONDS) 52 53 72: 55 type=109 (BONDS) 52 56 72: 56 type=110 (BONDS) 54 55 72: 57 type=109 (BONDS) 54 56 72: 58 type=110 (BONDS) 56 57 72: 59 type=105 (BONDS) 58 59 72: 60 type=106 (BONDS) 58 60 72: 61 type=100 (BONDS) 60 61 72: 62 type=107 (BONDS) 60 62 72: 63 type=102 (BONDS) 62 63 72: 64 type=102 (BONDS) 62 64 72: 65 type=104 (BONDS) 62 65 72: 66 type=105 (BONDS) 65 66 72: 67 type=106 (BONDS) 65 67 72: 68 type=100 (BONDS) 67 68 72: 69 type=107 (BONDS) 67 69 72: 70 type=102 (BONDS) 69 70 72: 71 type=103 (BONDS) 69 71 72: 72 type=104 (BONDS) 69 89 72: 73 type=102 (BONDS) 71 72 72: 74 type=102 (BONDS) 71 73 72: 75 type=103 (BONDS) 71 74 72: 76 type=102 (BONDS) 74 75 72: 77 type=102 (BONDS) 74 76 72: 78 type=103 (BONDS) 74 77 72: 79 type=102 (BONDS) 77 78 72: 80 type=102 (BONDS) 77 79 72: 81 type=111 (BONDS) 77 80 72: 82 type=100 (BONDS) 80 81 72: 83 type=112 (BONDS) 80 82 72: 84 type=112 (BONDS) 82 83 72: 85 type=112 (BONDS) 82 86 72: 86 type=100 (BONDS) 83 84 72: 87 type=100 (BONDS) 83 85 72: 88 type=100 (BONDS) 86 87 72: 89 type=100 (BONDS) 86 88 72: 90 type=105 (BONDS) 89 90 72: 91 type=106 (BONDS) 89 91 72: 92 type=100 (BONDS) 91 92 72: 93 type=107 (BONDS) 91 93 72: 94 type=102 (BONDS) 93 94 72: 95 type=103 (BONDS) 93 95 72: 96 type=104 (BONDS) 93 100 72: 97 type=102 (BONDS) 95 96 72: 98 type=102 (BONDS) 95 97 72: 99 type=113 (BONDS) 95 98 72: 100 type=114 (BONDS) 98 99 72: 101 type=105 (BONDS) 100 101 72: 102 type=106 (BONDS) 100 102 72: 103 type=100 (BONDS) 102 103 72: 104 type=107 (BONDS) 102 104 72: 105 type=102 (BONDS) 104 105 72: 106 type=103 (BONDS) 104 106 72: 107 type=104 (BONDS) 104 115 72: 108 type=102 (BONDS) 106 107 72: 109 type=102 (BONDS) 106 108 72: 110 type=103 (BONDS) 106 109 72: 111 type=102 (BONDS) 109 110 72: 112 type=102 (BONDS) 109 111 72: 113 type=104 (BONDS) 109 112 72: 114 type=115 (BONDS) 112 113 72: 115 type=115 (BONDS) 112 114 72: 116 type=105 (BONDS) 115 116 72: 117 type=106 (BONDS) 115 117 72: 118 type=100 (BONDS) 117 118 72: 119 type=107 (BONDS) 117 119 72: 120 type=102 (BONDS) 119 120 72: 121 type=103 (BONDS) 119 121 72: 122 type=104 (BONDS) 119 134 72: 123 type=102 (BONDS) 121 122 72: 124 type=102 (BONDS) 121 123 72: 125 type=103 (BONDS) 121 124 72: 126 type=102 (BONDS) 124 125 72: 127 type=103 (BONDS) 124 126 72: 128 type=103 (BONDS) 124 130 72: 129 type=102 (BONDS) 126 127 72: 130 type=102 (BONDS) 126 128 72: 131 type=102 (BONDS) 126 129 72: 132 type=102 (BONDS) 130 131 72: 133 type=102 (BONDS) 130 132 72: 134 type=102 (BONDS) 130 133 72: 135 type=105 (BONDS) 134 135 72: 136 type=106 (BONDS) 134 136 72: 137 type=100 (BONDS) 136 137 72: 138 type=107 (BONDS) 136 138 72: 139 type=102 (BONDS) 138 139 72: 140 type=103 (BONDS) 138 140 72: 141 type=104 (BONDS) 138 144 72: 142 type=102 (BONDS) 140 141 72: 143 type=102 (BONDS) 140 142 72: 144 type=102 (BONDS) 140 143 72: 145 type=105 (BONDS) 144 145 72: 146 type=106 (BONDS) 144 146 72: 147 type=100 (BONDS) 146 147 72: 148 type=107 (BONDS) 146 148 72: 149 type=102 (BONDS) 148 149 72: 150 type=103 (BONDS) 148 150 72: 151 type=104 (BONDS) 148 154 72: 152 type=102 (BONDS) 150 151 72: 153 type=102 (BONDS) 150 152 72: 154 type=102 (BONDS) 150 153 72: 155 type=105 (BONDS) 154 155 72: G96Bond: 72: nr: 0 72: Morse: 72: nr: 0 72: Cubic Bonds: 72: nr: 0 72: Connect Bonds: 72: nr: 0 72: Harmonic Pot.: 72: nr: 0 72: FENE Bonds: 72: nr: 0 72: Tab. Bonds: 72: nr: 0 72: Tab. Bonds NC: 72: nr: 0 72: Restraint Pot.: 72: nr: 0 72: Angle: 72: nr: 1124 72: iatoms: 72: 0 type=116 (ANGLES) 1 0 2 72: 1 type=116 (ANGLES) 1 0 3 72: 2 type=116 (ANGLES) 1 0 4 72: 3 type=116 (ANGLES) 2 0 3 72: 4 type=116 (ANGLES) 2 0 4 72: 5 type=116 (ANGLES) 3 0 4 72: 6 type=116 (ANGLES) 0 4 5 72: 7 type=117 (ANGLES) 0 4 6 72: 8 type=117 (ANGLES) 0 4 22 72: 9 type=118 (ANGLES) 5 4 6 72: 10 type=116 (ANGLES) 5 4 22 72: 11 type=119 (ANGLES) 6 4 22 72: 12 type=118 (ANGLES) 4 6 7 72: 13 type=118 (ANGLES) 4 6 8 72: 14 type=120 (ANGLES) 4 6 9 72: 15 type=121 (ANGLES) 7 6 8 72: 16 type=118 (ANGLES) 7 6 9 72: 17 type=118 (ANGLES) 8 6 9 72: 18 type=118 (ANGLES) 6 9 10 72: 19 type=118 (ANGLES) 6 9 11 72: 20 type=120 (ANGLES) 6 9 12 72: 21 type=121 (ANGLES) 10 9 11 72: 22 type=118 (ANGLES) 10 9 12 72: 23 type=118 (ANGLES) 11 9 12 72: 24 type=118 (ANGLES) 9 12 13 72: 25 type=118 (ANGLES) 9 12 14 72: 26 type=120 (ANGLES) 9 12 15 72: 27 type=121 (ANGLES) 13 12 14 72: 28 type=118 (ANGLES) 13 12 15 72: 29 type=118 (ANGLES) 14 12 15 72: 30 type=118 (ANGLES) 12 15 16 72: 31 type=118 (ANGLES) 12 15 17 72: 32 type=117 (ANGLES) 12 15 18 72: 33 type=121 (ANGLES) 16 15 17 72: 34 type=116 (ANGLES) 16 15 18 72: 35 type=116 (ANGLES) 17 15 18 72: 36 type=116 (ANGLES) 15 18 19 72: 37 type=116 (ANGLES) 15 18 20 72: 38 type=116 (ANGLES) 15 18 21 72: 39 type=116 (ANGLES) 19 18 20 72: 40 type=116 (ANGLES) 19 18 21 72: 41 type=116 (ANGLES) 20 18 21 72: 42 type=122 (ANGLES) 4 22 23 72: 43 type=123 (ANGLES) 4 22 24 72: 44 type=124 (ANGLES) 23 22 24 72: 45 type=125 (ANGLES) 22 24 25 72: 46 type=126 (ANGLES) 22 24 26 72: 47 type=127 (ANGLES) 25 24 26 72: 48 type=116 (ANGLES) 24 26 27 72: 49 type=128 (ANGLES) 24 26 28 72: 50 type=129 (ANGLES) 24 26 38 72: 51 type=118 (ANGLES) 27 26 28 72: 52 type=116 (ANGLES) 27 26 38 72: 53 type=119 (ANGLES) 28 26 38 72: 54 type=118 (ANGLES) 26 28 29 72: 55 type=120 (ANGLES) 26 28 30 72: 56 type=120 (ANGLES) 26 28 34 72: 57 type=118 (ANGLES) 29 28 30 72: 58 type=118 (ANGLES) 29 28 34 72: 59 type=120 (ANGLES) 30 28 34 72: 60 type=118 (ANGLES) 28 30 31 72: 61 type=118 (ANGLES) 28 30 32 72: 62 type=118 (ANGLES) 28 30 33 72: 63 type=121 (ANGLES) 31 30 32 72: 64 type=121 (ANGLES) 31 30 33 72: 65 type=121 (ANGLES) 32 30 33 72: 66 type=118 (ANGLES) 28 34 35 72: 67 type=118 (ANGLES) 28 34 36 72: 68 type=118 (ANGLES) 28 34 37 72: 69 type=121 (ANGLES) 35 34 36 72: 70 type=121 (ANGLES) 35 34 37 72: 71 type=121 (ANGLES) 36 34 37 72: 72 type=122 (ANGLES) 26 38 39 72: 73 type=123 (ANGLES) 26 38 40 72: 74 type=124 (ANGLES) 39 38 40 72: 75 type=125 (ANGLES) 38 40 41 72: 76 type=126 (ANGLES) 38 40 42 72: 77 type=127 (ANGLES) 41 40 42 72: 78 type=116 (ANGLES) 40 42 43 72: 79 type=128 (ANGLES) 40 42 44 72: 80 type=129 (ANGLES) 40 42 58 72: 81 type=118 (ANGLES) 43 42 44 72: 82 type=116 (ANGLES) 43 42 58 72: 83 type=119 (ANGLES) 44 42 58 72: 84 type=118 (ANGLES) 42 44 45 72: 85 type=118 (ANGLES) 42 44 46 72: 86 type=130 (ANGLES) 42 44 47 72: 87 type=121 (ANGLES) 45 44 46 72: 88 type=116 (ANGLES) 45 44 47 72: 89 type=116 (ANGLES) 46 44 47 72: 90 type=131 (ANGLES) 44 47 48 72: 91 type=131 (ANGLES) 44 47 50 72: 92 type=132 (ANGLES) 48 47 50 72: 93 type=133 (ANGLES) 47 48 49 72: 94 type=132 (ANGLES) 47 48 52 72: 95 type=133 (ANGLES) 49 48 52 72: 96 type=133 (ANGLES) 47 50 51 72: 97 type=132 (ANGLES) 47 50 54 72: 98 type=133 (ANGLES) 51 50 54 72: 99 type=133 (ANGLES) 48 52 53 72: 100 type=132 (ANGLES) 48 52 56 72: 101 type=133 (ANGLES) 53 52 56 72: 102 type=133 (ANGLES) 50 54 55 72: 103 type=132 (ANGLES) 50 54 56 72: 104 type=133 (ANGLES) 55 54 56 72: 105 type=132 (ANGLES) 52 56 54 72: 106 type=133 (ANGLES) 52 56 57 72: 107 type=133 (ANGLES) 54 56 57 72: 108 type=122 (ANGLES) 42 58 59 72: 109 type=123 (ANGLES) 42 58 60 72: 110 type=124 (ANGLES) 59 58 60 72: 111 type=125 (ANGLES) 58 60 61 72: 112 type=126 (ANGLES) 58 60 62 72: 113 type=127 (ANGLES) 61 60 62 72: 114 type=116 (ANGLES) 60 62 63 72: 115 type=116 (ANGLES) 60 62 64 72: 116 type=129 (ANGLES) 60 62 65 72: 117 type=121 (ANGLES) 63 62 64 72: 118 type=116 (ANGLES) 63 62 65 72: 119 type=116 (ANGLES) 64 62 65 72: 120 type=122 (ANGLES) 62 65 66 72: 121 type=123 (ANGLES) 62 65 67 72: 122 type=124 (ANGLES) 66 65 67 72: 123 type=125 (ANGLES) 65 67 68 72: 124 type=126 (ANGLES) 65 67 69 72: 125 type=127 (ANGLES) 68 67 69 72: 126 type=116 (ANGLES) 67 69 70 72: 127 type=128 (ANGLES) 67 69 71 72: 128 type=129 (ANGLES) 67 69 89 72: 129 type=118 (ANGLES) 70 69 71 72: 130 type=116 (ANGLES) 70 69 89 72: 131 type=119 (ANGLES) 71 69 89 72: 132 type=118 (ANGLES) 69 71 72 72: 133 type=118 (ANGLES) 69 71 73 72: 134 type=120 (ANGLES) 69 71 74 72: 135 type=121 (ANGLES) 72 71 73 72: 136 type=118 (ANGLES) 72 71 74 72: 137 type=118 (ANGLES) 73 71 74 72: 138 type=118 (ANGLES) 71 74 75 72: 139 type=118 (ANGLES) 71 74 76 72: 140 type=120 (ANGLES) 71 74 77 72: 141 type=121 (ANGLES) 75 74 76 72: 142 type=118 (ANGLES) 75 74 77 72: 143 type=118 (ANGLES) 76 74 77 72: 144 type=118 (ANGLES) 74 77 78 72: 145 type=118 (ANGLES) 74 77 79 72: 146 type=117 (ANGLES) 74 77 80 72: 147 type=121 (ANGLES) 78 77 79 72: 148 type=116 (ANGLES) 78 77 80 72: 149 type=116 (ANGLES) 79 77 80 72: 150 type=134 (ANGLES) 77 80 81 72: 151 type=135 (ANGLES) 77 80 82 72: 152 type=133 (ANGLES) 81 80 82 72: 153 type=131 (ANGLES) 80 82 83 72: 154 type=131 (ANGLES) 80 82 86 72: 155 type=131 (ANGLES) 83 82 86 72: 156 type=133 (ANGLES) 82 83 84 72: 157 type=133 (ANGLES) 82 83 85 72: 158 type=133 (ANGLES) 84 83 85 72: 159 type=133 (ANGLES) 82 86 87 72: 160 type=133 (ANGLES) 82 86 88 72: 161 type=133 (ANGLES) 87 86 88 72: 162 type=122 (ANGLES) 69 89 90 72: 163 type=123 (ANGLES) 69 89 91 72: 164 type=124 (ANGLES) 90 89 91 72: 165 type=125 (ANGLES) 89 91 92 72: 166 type=126 (ANGLES) 89 91 93 72: 167 type=127 (ANGLES) 92 91 93 72: 168 type=116 (ANGLES) 91 93 94 72: 169 type=128 (ANGLES) 91 93 95 72: 170 type=129 (ANGLES) 91 93 100 72: 171 type=118 (ANGLES) 94 93 95 72: 172 type=116 (ANGLES) 94 93 100 72: 173 type=119 (ANGLES) 95 93 100 72: 174 type=118 (ANGLES) 93 95 96 72: 175 type=118 (ANGLES) 93 95 97 72: 176 type=136 (ANGLES) 93 95 98 72: 177 type=121 (ANGLES) 96 95 97 72: 178 type=116 (ANGLES) 96 95 98 72: 179 type=116 (ANGLES) 97 95 98 72: 180 type=137 (ANGLES) 95 98 99 72: 181 type=122 (ANGLES) 93 100 101 72: 182 type=123 (ANGLES) 93 100 102 72: 183 type=124 (ANGLES) 101 100 102 72: 184 type=125 (ANGLES) 100 102 103 72: 185 type=126 (ANGLES) 100 102 104 72: 186 type=127 (ANGLES) 103 102 104 72: 187 type=116 (ANGLES) 102 104 105 72: 188 type=128 (ANGLES) 102 104 106 72: 189 type=129 (ANGLES) 102 104 115 72: 190 type=118 (ANGLES) 105 104 106 72: 191 type=116 (ANGLES) 105 104 115 72: 192 type=119 (ANGLES) 106 104 115 72: 193 type=118 (ANGLES) 104 106 107 72: 194 type=118 (ANGLES) 104 106 108 72: 195 type=120 (ANGLES) 104 106 109 72: 196 type=121 (ANGLES) 107 106 108 72: 197 type=118 (ANGLES) 107 106 109 72: 198 type=118 (ANGLES) 108 106 109 72: 199 type=118 (ANGLES) 106 109 110 72: 200 type=118 (ANGLES) 106 109 111 72: 201 type=119 (ANGLES) 106 109 112 72: 202 type=121 (ANGLES) 110 109 111 72: 203 type=116 (ANGLES) 110 109 112 72: 204 type=116 (ANGLES) 111 109 112 72: 205 type=138 (ANGLES) 109 112 113 72: 206 type=138 (ANGLES) 109 112 114 72: 207 type=139 (ANGLES) 113 112 114 72: 208 type=122 (ANGLES) 104 115 116 72: 209 type=123 (ANGLES) 104 115 117 72: 210 type=124 (ANGLES) 116 115 117 72: 211 type=125 (ANGLES) 115 117 118 72: 212 type=126 (ANGLES) 115 117 119 72: 213 type=127 (ANGLES) 118 117 119 72: 214 type=116 (ANGLES) 117 119 120 72: 215 type=128 (ANGLES) 117 119 121 72: 216 type=129 (ANGLES) 117 119 134 72: 217 type=118 (ANGLES) 120 119 121 72: 218 type=116 (ANGLES) 120 119 134 72: 219 type=119 (ANGLES) 121 119 134 72: 220 type=118 (ANGLES) 119 121 122 72: 221 type=118 (ANGLES) 119 121 123 72: 222 type=120 (ANGLES) 119 121 124 72: 223 type=121 (ANGLES) 122 121 123 72: 224 type=118 (ANGLES) 122 121 124 72: 225 type=118 (ANGLES) 123 121 124 72: 226 type=118 (ANGLES) 121 124 125 72: 227 type=120 (ANGLES) 121 124 126 72: 228 type=120 (ANGLES) 121 124 130 72: 229 type=118 (ANGLES) 125 124 126 72: 230 type=118 (ANGLES) 125 124 130 72: 231 type=120 (ANGLES) 126 124 130 72: 232 type=118 (ANGLES) 124 126 127 72: 233 type=118 (ANGLES) 124 126 128 72: 234 type=118 (ANGLES) 124 126 129 72: 235 type=121 (ANGLES) 127 126 128 72: 236 type=121 (ANGLES) 127 126 129 72: 237 type=121 (ANGLES) 128 126 129 72: 238 type=118 (ANGLES) 124 130 131 72: 239 type=118 (ANGLES) 124 130 132 72: 240 type=118 (ANGLES) 124 130 133 72: 241 type=121 (ANGLES) 131 130 132 72: 242 type=121 (ANGLES) 131 130 133 72: 243 type=121 (ANGLES) 132 130 133 72: 244 type=122 (ANGLES) 119 134 135 72: 245 type=123 (ANGLES) 119 134 136 72: 246 type=124 (ANGLES) 135 134 136 72: 247 type=125 (ANGLES) 134 136 137 72: 248 type=126 (ANGLES) 134 136 138 72: 249 type=127 (ANGLES) 137 136 138 72: 250 type=116 (ANGLES) 136 138 139 72: 251 type=128 (ANGLES) 136 138 140 72: 252 type=129 (ANGLES) 136 138 144 72: 253 type=118 (ANGLES) 139 138 140 72: 254 type=116 (ANGLES) 139 138 144 72: 255 type=119 (ANGLES) 140 138 144 72: 256 type=118 (ANGLES) 138 140 141 72: 257 type=118 (ANGLES) 138 140 142 72: 258 type=118 (ANGLES) 138 140 143 72: 259 type=121 (ANGLES) 141 140 142 72: 260 type=121 (ANGLES) 141 140 143 72: 261 type=121 (ANGLES) 142 140 143 72: 262 type=122 (ANGLES) 138 144 145 72: 263 type=123 (ANGLES) 138 144 146 72: 264 type=124 (ANGLES) 145 144 146 72: 265 type=125 (ANGLES) 144 146 147 72: 266 type=126 (ANGLES) 144 146 148 72: 267 type=127 (ANGLES) 147 146 148 72: 268 type=116 (ANGLES) 146 148 149 72: 269 type=128 (ANGLES) 146 148 150 72: 270 type=129 (ANGLES) 146 148 154 72: 271 type=118 (ANGLES) 149 148 150 72: 272 type=116 (ANGLES) 149 148 154 72: 273 type=119 (ANGLES) 150 148 154 72: 274 type=118 (ANGLES) 148 150 151 72: 275 type=118 (ANGLES) 148 150 152 72: 276 type=118 (ANGLES) 148 150 153 72: 277 type=121 (ANGLES) 151 150 152 72: 278 type=121 (ANGLES) 151 150 153 72: 279 type=121 (ANGLES) 152 150 153 72: 280 type=122 (ANGLES) 148 154 155 72: G96Angle: 72: nr: 0 72: Restr. Angles: 72: nr: 0 72: Lin. Angle: 72: nr: 0 72: Bond-Cross: 72: nr: 0 72: BA-Cross: 72: nr: 0 72: U-B: 72: nr: 0 72: Quartic Angles: 72: nr: 0 72: Tab. Angles: 72: nr: 0 72: Proper Dih.: 72: nr: 145 72: iatoms: 72: 0 type=140 (PDIHS) 4 24 22 23 72: 1 type=141 (PDIHS) 22 26 24 25 72: 2 type=140 (PDIHS) 26 40 38 39 72: 3 type=141 (PDIHS) 38 42 40 41 72: 4 type=140 (PDIHS) 42 60 58 59 72: 5 type=142 (PDIHS) 44 47 50 48 72: 6 type=142 (PDIHS) 47 52 48 49 72: 7 type=142 (PDIHS) 47 54 50 51 72: 8 type=142 (PDIHS) 48 56 52 53 72: 9 type=142 (PDIHS) 50 56 54 55 72: 10 type=142 (PDIHS) 52 54 56 57 72: 11 type=141 (PDIHS) 58 62 60 61 72: 12 type=140 (PDIHS) 62 67 65 66 72: 13 type=141 (PDIHS) 65 69 67 68 72: 14 type=140 (PDIHS) 69 91 89 90 72: 15 type=141 (PDIHS) 77 82 80 81 72: 16 type=140 (PDIHS) 80 83 82 86 72: 17 type=141 (PDIHS) 82 84 83 85 72: 18 type=141 (PDIHS) 82 87 86 88 72: 19 type=141 (PDIHS) 89 93 91 92 72: 20 type=140 (PDIHS) 93 102 100 101 72: 21 type=141 (PDIHS) 100 104 102 103 72: 22 type=140 (PDIHS) 104 117 115 116 72: 23 type=140 (PDIHS) 109 113 112 114 72: 24 type=141 (PDIHS) 115 119 117 118 72: 25 type=140 (PDIHS) 119 136 134 135 72: 26 type=141 (PDIHS) 134 138 136 137 72: 27 type=140 (PDIHS) 138 146 144 145 72: 28 type=141 (PDIHS) 144 148 146 147 72: Ryckaert-Bell.: 72: nr: 1565 72: iatoms: 72: 0 type=143 (RBDIHS) 1 0 4 5 72: 1 type=144 (RBDIHS) 1 0 4 6 72: 2 type=144 (RBDIHS) 1 0 4 22 72: 3 type=143 (RBDIHS) 2 0 4 5 72: 4 type=144 (RBDIHS) 2 0 4 6 72: 5 type=144 (RBDIHS) 2 0 4 22 72: 6 type=143 (RBDIHS) 3 0 4 5 72: 7 type=144 (RBDIHS) 3 0 4 6 72: 8 type=144 (RBDIHS) 3 0 4 22 72: 9 type=145 (RBDIHS) 0 4 6 9 72: 10 type=146 (RBDIHS) 22 4 6 9 72: 11 type=147 (RBDIHS) 0 4 6 7 72: 12 type=147 (RBDIHS) 0 4 6 8 72: 13 type=148 (RBDIHS) 5 4 6 7 72: 14 type=148 (RBDIHS) 5 4 6 8 72: 15 type=148 (RBDIHS) 5 4 6 9 72: 16 type=149 (RBDIHS) 22 4 6 7 72: 17 type=149 (RBDIHS) 22 4 6 8 72: 18 type=150 (RBDIHS) 0 4 22 24 72: 19 type=151 (RBDIHS) 6 4 22 24 72: 20 type=148 (RBDIHS) 4 6 9 10 72: 21 type=148 (RBDIHS) 4 6 9 11 72: 22 type=152 (RBDIHS) 4 6 9 12 72: 23 type=148 (RBDIHS) 7 6 9 10 72: 24 type=148 (RBDIHS) 7 6 9 11 72: 25 type=148 (RBDIHS) 7 6 9 12 72: 26 type=148 (RBDIHS) 8 6 9 10 72: 27 type=148 (RBDIHS) 8 6 9 11 72: 28 type=148 (RBDIHS) 8 6 9 12 72: 29 type=148 (RBDIHS) 6 9 12 13 72: 30 type=148 (RBDIHS) 6 9 12 14 72: 31 type=152 (RBDIHS) 6 9 12 15 72: 32 type=148 (RBDIHS) 10 9 12 13 72: 33 type=148 (RBDIHS) 10 9 12 14 72: 34 type=148 (RBDIHS) 10 9 12 15 72: 35 type=148 (RBDIHS) 11 9 12 13 72: 36 type=148 (RBDIHS) 11 9 12 14 72: 37 type=148 (RBDIHS) 11 9 12 15 72: 38 type=148 (RBDIHS) 9 12 15 16 72: 39 type=148 (RBDIHS) 9 12 15 17 72: 40 type=153 (RBDIHS) 9 12 15 18 72: 41 type=148 (RBDIHS) 13 12 15 16 72: 42 type=148 (RBDIHS) 13 12 15 17 72: 43 type=154 (RBDIHS) 13 12 15 18 72: 44 type=148 (RBDIHS) 14 12 15 16 72: 45 type=148 (RBDIHS) 14 12 15 17 72: 46 type=154 (RBDIHS) 14 12 15 18 72: 47 type=144 (RBDIHS) 12 15 18 19 72: 48 type=144 (RBDIHS) 12 15 18 20 72: 49 type=144 (RBDIHS) 12 15 18 21 72: 50 type=143 (RBDIHS) 16 15 18 19 72: 51 type=143 (RBDIHS) 16 15 18 20 72: 52 type=143 (RBDIHS) 16 15 18 21 72: 53 type=143 (RBDIHS) 17 15 18 19 72: 54 type=143 (RBDIHS) 17 15 18 20 72: 55 type=143 (RBDIHS) 17 15 18 21 72: 56 type=155 (RBDIHS) 4 22 24 25 72: 57 type=156 (RBDIHS) 4 22 24 26 72: 58 type=155 (RBDIHS) 23 22 24 25 72: 59 type=157 (RBDIHS) 23 22 24 26 72: 60 type=158 (RBDIHS) 22 24 26 28 72: 61 type=159 (RBDIHS) 22 24 26 38 72: 62 type=160 (RBDIHS) 24 26 28 30 72: 63 type=160 (RBDIHS) 24 26 28 34 72: 64 type=161 (RBDIHS) 38 26 28 30 72: 65 type=161 (RBDIHS) 38 26 28 34 72: 66 type=147 (RBDIHS) 24 26 28 29 72: 67 type=148 (RBDIHS) 27 26 28 29 72: 68 type=148 (RBDIHS) 27 26 28 30 72: 69 type=148 (RBDIHS) 27 26 28 34 72: 70 type=149 (RBDIHS) 38 26 28 29 72: 71 type=150 (RBDIHS) 24 26 38 40 72: 72 type=151 (RBDIHS) 28 26 38 40 72: 73 type=148 (RBDIHS) 26 28 30 31 72: 74 type=148 (RBDIHS) 26 28 30 32 72: 75 type=148 (RBDIHS) 26 28 30 33 72: 76 type=148 (RBDIHS) 29 28 30 31 72: 77 type=148 (RBDIHS) 29 28 30 32 72: 78 type=148 (RBDIHS) 29 28 30 33 72: 79 type=148 (RBDIHS) 34 28 30 31 72: 80 type=148 (RBDIHS) 34 28 30 32 72: 81 type=148 (RBDIHS) 34 28 30 33 72: 82 type=148 (RBDIHS) 26 28 34 35 72: 83 type=148 (RBDIHS) 26 28 34 36 72: 84 type=148 (RBDIHS) 26 28 34 37 72: 85 type=148 (RBDIHS) 29 28 34 35 72: 86 type=148 (RBDIHS) 29 28 34 36 72: 87 type=148 (RBDIHS) 29 28 34 37 72: 88 type=148 (RBDIHS) 30 28 34 35 72: 89 type=148 (RBDIHS) 30 28 34 36 72: 90 type=148 (RBDIHS) 30 28 34 37 72: 91 type=155 (RBDIHS) 26 38 40 41 72: 92 type=156 (RBDIHS) 26 38 40 42 72: 93 type=155 (RBDIHS) 39 38 40 41 72: 94 type=157 (RBDIHS) 39 38 40 42 72: 95 type=158 (RBDIHS) 38 40 42 44 72: 96 type=159 (RBDIHS) 38 40 42 58 72: 97 type=147 (RBDIHS) 40 42 44 45 72: 98 type=147 (RBDIHS) 40 42 44 46 72: 99 type=162 (RBDIHS) 40 42 44 47 72: 100 type=148 (RBDIHS) 43 42 44 45 72: 101 type=148 (RBDIHS) 43 42 44 46 72: 102 type=163 (RBDIHS) 43 42 44 47 72: 103 type=149 (RBDIHS) 58 42 44 45 72: 104 type=149 (RBDIHS) 58 42 44 46 72: 105 type=164 (RBDIHS) 58 42 44 47 72: 106 type=150 (RBDIHS) 40 42 58 60 72: 107 type=151 (RBDIHS) 44 42 58 60 72: 108 type=165 (RBDIHS) 44 47 48 49 72: 109 type=165 (RBDIHS) 44 47 48 52 72: 110 type=165 (RBDIHS) 50 47 48 49 72: 111 type=165 (RBDIHS) 50 47 48 52 72: 112 type=165 (RBDIHS) 44 47 50 51 72: 113 type=165 (RBDIHS) 44 47 50 54 72: 114 type=165 (RBDIHS) 48 47 50 51 72: 115 type=165 (RBDIHS) 48 47 50 54 72: 116 type=165 (RBDIHS) 47 48 52 53 72: 117 type=165 (RBDIHS) 47 48 52 56 72: 118 type=165 (RBDIHS) 49 48 52 53 72: 119 type=165 (RBDIHS) 49 48 52 56 72: 120 type=165 (RBDIHS) 47 50 54 55 72: 121 type=165 (RBDIHS) 47 50 54 56 72: 122 type=165 (RBDIHS) 51 50 54 55 72: 123 type=165 (RBDIHS) 51 50 54 56 72: 124 type=165 (RBDIHS) 48 52 56 54 72: 125 type=165 (RBDIHS) 48 52 56 57 72: 126 type=165 (RBDIHS) 53 52 56 54 72: 127 type=165 (RBDIHS) 53 52 56 57 72: 128 type=165 (RBDIHS) 50 54 56 52 72: 129 type=165 (RBDIHS) 50 54 56 57 72: 130 type=165 (RBDIHS) 55 54 56 52 72: 131 type=165 (RBDIHS) 55 54 56 57 72: 132 type=155 (RBDIHS) 42 58 60 61 72: 133 type=156 (RBDIHS) 42 58 60 62 72: 134 type=155 (RBDIHS) 59 58 60 61 72: 135 type=157 (RBDIHS) 59 58 60 62 72: 136 type=159 (RBDIHS) 58 60 62 65 72: 137 type=150 (RBDIHS) 60 62 65 67 72: 138 type=155 (RBDIHS) 62 65 67 68 72: 139 type=156 (RBDIHS) 62 65 67 69 72: 140 type=155 (RBDIHS) 66 65 67 68 72: 141 type=157 (RBDIHS) 66 65 67 69 72: 142 type=158 (RBDIHS) 65 67 69 71 72: 143 type=159 (RBDIHS) 65 67 69 89 72: 144 type=166 (RBDIHS) 67 69 71 74 72: 145 type=167 (RBDIHS) 89 69 71 74 72: 146 type=147 (RBDIHS) 67 69 71 72 72: 147 type=147 (RBDIHS) 67 69 71 73 72: 148 type=148 (RBDIHS) 70 69 71 72 72: 149 type=148 (RBDIHS) 70 69 71 73 72: 150 type=148 (RBDIHS) 70 69 71 74 72: 151 type=149 (RBDIHS) 89 69 71 72 72: 152 type=149 (RBDIHS) 89 69 71 73 72: 153 type=150 (RBDIHS) 67 69 89 91 72: 154 type=151 (RBDIHS) 71 69 89 91 72: 155 type=148 (RBDIHS) 69 71 74 75 72: 156 type=148 (RBDIHS) 69 71 74 76 72: 157 type=152 (RBDIHS) 69 71 74 77 72: 158 type=148 (RBDIHS) 72 71 74 75 72: 159 type=148 (RBDIHS) 72 71 74 76 72: 160 type=148 (RBDIHS) 72 71 74 77 72: 161 type=148 (RBDIHS) 73 71 74 75 72: 162 type=148 (RBDIHS) 73 71 74 76 72: 163 type=148 (RBDIHS) 73 71 74 77 72: 164 type=148 (RBDIHS) 71 74 77 78 72: 165 type=148 (RBDIHS) 71 74 77 79 72: 166 type=153 (RBDIHS) 71 74 77 80 72: 167 type=148 (RBDIHS) 75 74 77 78 72: 168 type=148 (RBDIHS) 75 74 77 79 72: 169 type=168 (RBDIHS) 75 74 77 80 72: 170 type=148 (RBDIHS) 76 74 77 78 72: 171 type=148 (RBDIHS) 76 74 77 79 72: 172 type=168 (RBDIHS) 76 74 77 80 72: 173 type=169 (RBDIHS) 74 77 80 81 72: 174 type=170 (RBDIHS) 74 77 80 82 72: 175 type=171 (RBDIHS) 78 77 80 82 72: 176 type=171 (RBDIHS) 79 77 80 82 72: 177 type=172 (RBDIHS) 77 80 82 83 72: 178 type=172 (RBDIHS) 77 80 82 86 72: 179 type=173 (RBDIHS) 81 80 82 83 72: 180 type=173 (RBDIHS) 81 80 82 86 72: 181 type=173 (RBDIHS) 80 82 83 84 72: 182 type=173 (RBDIHS) 80 82 83 85 72: 183 type=173 (RBDIHS) 86 82 83 84 72: 184 type=173 (RBDIHS) 86 82 83 85 72: 185 type=173 (RBDIHS) 80 82 86 87 72: 186 type=173 (RBDIHS) 80 82 86 88 72: 187 type=173 (RBDIHS) 83 82 86 87 72: 188 type=173 (RBDIHS) 83 82 86 88 72: 189 type=155 (RBDIHS) 69 89 91 92 72: 190 type=156 (RBDIHS) 69 89 91 93 72: 191 type=155 (RBDIHS) 90 89 91 92 72: 192 type=157 (RBDIHS) 90 89 91 93 72: 193 type=158 (RBDIHS) 89 91 93 95 72: 194 type=159 (RBDIHS) 89 91 93 100 72: 195 type=174 (RBDIHS) 91 93 95 98 72: 196 type=175 (RBDIHS) 100 93 95 98 72: 197 type=147 (RBDIHS) 91 93 95 96 72: 198 type=147 (RBDIHS) 91 93 95 97 72: 199 type=148 (RBDIHS) 94 93 95 96 72: 200 type=148 (RBDIHS) 94 93 95 97 72: 201 type=176 (RBDIHS) 94 93 95 98 72: 202 type=149 (RBDIHS) 100 93 95 96 72: 203 type=149 (RBDIHS) 100 93 95 97 72: 204 type=150 (RBDIHS) 91 93 100 102 72: 205 type=151 (RBDIHS) 95 93 100 102 72: 206 type=177 (RBDIHS) 93 95 98 99 72: 207 type=178 (RBDIHS) 96 95 98 99 72: 208 type=178 (RBDIHS) 97 95 98 99 72: 209 type=155 (RBDIHS) 93 100 102 103 72: 210 type=156 (RBDIHS) 93 100 102 104 72: 211 type=155 (RBDIHS) 101 100 102 103 72: 212 type=157 (RBDIHS) 101 100 102 104 72: 213 type=158 (RBDIHS) 100 102 104 106 72: 214 type=159 (RBDIHS) 100 102 104 115 72: 215 type=179 (RBDIHS) 102 104 106 109 72: 216 type=180 (RBDIHS) 115 104 106 109 72: 217 type=147 (RBDIHS) 102 104 106 107 72: 218 type=147 (RBDIHS) 102 104 106 108 72: 219 type=148 (RBDIHS) 105 104 106 107 72: 220 type=148 (RBDIHS) 105 104 106 108 72: 221 type=148 (RBDIHS) 105 104 106 109 72: 222 type=149 (RBDIHS) 115 104 106 107 72: 223 type=149 (RBDIHS) 115 104 106 108 72: 224 type=150 (RBDIHS) 102 104 115 117 72: 225 type=151 (RBDIHS) 106 104 115 117 72: 226 type=148 (RBDIHS) 104 106 109 110 72: 227 type=148 (RBDIHS) 104 106 109 111 72: 228 type=181 (RBDIHS) 104 106 109 112 72: 229 type=148 (RBDIHS) 107 106 109 110 72: 230 type=148 (RBDIHS) 107 106 109 111 72: 231 type=182 (RBDIHS) 107 106 109 112 72: 232 type=148 (RBDIHS) 108 106 109 110 72: 233 type=148 (RBDIHS) 108 106 109 111 72: 234 type=182 (RBDIHS) 108 106 109 112 72: 235 type=183 (RBDIHS) 106 109 112 113 72: 236 type=183 (RBDIHS) 106 109 112 114 72: 237 type=155 (RBDIHS) 104 115 117 118 72: 238 type=156 (RBDIHS) 104 115 117 119 72: 239 type=155 (RBDIHS) 116 115 117 118 72: 240 type=157 (RBDIHS) 116 115 117 119 72: 241 type=158 (RBDIHS) 115 117 119 121 72: 242 type=159 (RBDIHS) 115 117 119 134 72: 243 type=184 (RBDIHS) 117 119 121 124 72: 244 type=185 (RBDIHS) 134 119 121 124 72: 245 type=147 (RBDIHS) 117 119 121 122 72: 246 type=147 (RBDIHS) 117 119 121 123 72: 247 type=148 (RBDIHS) 120 119 121 122 72: 248 type=148 (RBDIHS) 120 119 121 123 72: 249 type=148 (RBDIHS) 120 119 121 124 72: 250 type=149 (RBDIHS) 134 119 121 122 72: 251 type=149 (RBDIHS) 134 119 121 123 72: 252 type=150 (RBDIHS) 117 119 134 136 72: 253 type=151 (RBDIHS) 121 119 134 136 72: 254 type=148 (RBDIHS) 119 121 124 125 72: 255 type=152 (RBDIHS) 119 121 124 126 72: 256 type=152 (RBDIHS) 119 121 124 130 72: 257 type=148 (RBDIHS) 122 121 124 125 72: 258 type=148 (RBDIHS) 122 121 124 126 72: 259 type=148 (RBDIHS) 122 121 124 130 72: 260 type=148 (RBDIHS) 123 121 124 125 72: 261 type=148 (RBDIHS) 123 121 124 126 72: 262 type=148 (RBDIHS) 123 121 124 130 72: 263 type=148 (RBDIHS) 121 124 126 127 72: 264 type=148 (RBDIHS) 121 124 126 128 72: 265 type=148 (RBDIHS) 121 124 126 129 72: 266 type=148 (RBDIHS) 125 124 126 127 72: 267 type=148 (RBDIHS) 125 124 126 128 72: 268 type=148 (RBDIHS) 125 124 126 129 72: 269 type=148 (RBDIHS) 130 124 126 127 72: 270 type=148 (RBDIHS) 130 124 126 128 72: 271 type=148 (RBDIHS) 130 124 126 129 72: 272 type=148 (RBDIHS) 121 124 130 131 72: 273 type=148 (RBDIHS) 121 124 130 132 72: 274 type=148 (RBDIHS) 121 124 130 133 72: 275 type=148 (RBDIHS) 125 124 130 131 72: 276 type=148 (RBDIHS) 125 124 130 132 72: 277 type=148 (RBDIHS) 125 124 130 133 72: 278 type=148 (RBDIHS) 126 124 130 131 72: 279 type=148 (RBDIHS) 126 124 130 132 72: 280 type=148 (RBDIHS) 126 124 130 133 72: 281 type=155 (RBDIHS) 119 134 136 137 72: 282 type=156 (RBDIHS) 119 134 136 138 72: 283 type=155 (RBDIHS) 135 134 136 137 72: 284 type=157 (RBDIHS) 135 134 136 138 72: 285 type=158 (RBDIHS) 134 136 138 140 72: 286 type=159 (RBDIHS) 134 136 138 144 72: 287 type=147 (RBDIHS) 136 138 140 141 72: 288 type=147 (RBDIHS) 136 138 140 142 72: 289 type=147 (RBDIHS) 136 138 140 143 72: 290 type=148 (RBDIHS) 139 138 140 141 72: 291 type=148 (RBDIHS) 139 138 140 142 72: 292 type=148 (RBDIHS) 139 138 140 143 72: 293 type=149 (RBDIHS) 144 138 140 141 72: 294 type=149 (RBDIHS) 144 138 140 142 72: 295 type=149 (RBDIHS) 144 138 140 143 72: 296 type=150 (RBDIHS) 136 138 144 146 72: 297 type=151 (RBDIHS) 140 138 144 146 72: 298 type=155 (RBDIHS) 138 144 146 147 72: 299 type=156 (RBDIHS) 138 144 146 148 72: 300 type=155 (RBDIHS) 145 144 146 147 72: 301 type=157 (RBDIHS) 145 144 146 148 72: 302 type=158 (RBDIHS) 144 146 148 150 72: 303 type=159 (RBDIHS) 144 146 148 154 72: 304 type=147 (RBDIHS) 146 148 150 151 72: 305 type=147 (RBDIHS) 146 148 150 152 72: 306 type=147 (RBDIHS) 146 148 150 153 72: 307 type=148 (RBDIHS) 149 148 150 151 72: 308 type=148 (RBDIHS) 149 148 150 152 72: 309 type=148 (RBDIHS) 149 148 150 153 72: 310 type=149 (RBDIHS) 154 148 150 151 72: 311 type=149 (RBDIHS) 154 148 150 152 72: 312 type=149 (RBDIHS) 154 148 150 153 72: Restr. Dih.: 72: nr: 0 72: CBT Dih.: 72: nr: 0 72: Fourier Dih.: 72: nr: 0 72: Improper Dih.: 72: nr: 0 72: Per. Imp. Dih.: 72: nr: 0 72: Tab. Dih.: 72: nr: 0 72: CMAP Dih.: 72: nr: 0 72: GB 1-2 Pol.: 72: nr: 0 72: GB 1-3 Pol.: 72: nr: 0 72: GB 1-4 Pol.: 72: nr: 0 72: GB Polariz.: 72: nr: 0 72: Nonpolar Sol.: 72: nr: 0 72: LJ-14: 72: nr: 1197 72: iatoms: 72: 0 type=186 (LJ14) 0 7 72: 1 type=186 (LJ14) 0 8 72: 2 type=187 (LJ14) 0 9 72: 3 type=188 (LJ14) 0 23 72: 4 type=189 (LJ14) 0 24 72: 5 type=190 (LJ14) 1 5 72: 6 type=190 (LJ14) 1 6 72: 7 type=190 (LJ14) 1 22 72: 8 type=190 (LJ14) 2 5 72: 9 type=190 (LJ14) 2 6 72: 10 type=190 (LJ14) 2 22 72: 11 type=190 (LJ14) 3 5 72: 12 type=190 (LJ14) 3 6 72: 13 type=190 (LJ14) 3 22 72: 14 type=191 (LJ14) 4 10 72: 15 type=191 (LJ14) 4 11 72: 16 type=192 (LJ14) 4 12 72: 17 type=190 (LJ14) 4 25 72: 18 type=192 (LJ14) 4 26 72: 19 type=193 (LJ14) 5 7 72: 20 type=193 (LJ14) 5 8 72: 21 type=191 (LJ14) 5 9 72: 22 type=194 (LJ14) 5 23 72: 23 type=186 (LJ14) 5 24 72: 24 type=191 (LJ14) 6 13 72: 25 type=191 (LJ14) 6 14 72: 26 type=192 (LJ14) 6 15 72: 27 type=195 (LJ14) 6 23 72: 28 type=187 (LJ14) 6 24 72: 29 type=193 (LJ14) 7 10 72: 30 type=193 (LJ14) 7 11 72: 31 type=191 (LJ14) 7 12 72: 32 type=196 (LJ14) 7 22 72: 33 type=193 (LJ14) 8 10 72: 34 type=193 (LJ14) 8 11 72: 35 type=191 (LJ14) 8 12 72: 36 type=196 (LJ14) 8 22 72: 37 type=191 (LJ14) 9 16 72: 38 type=191 (LJ14) 9 17 72: 39 type=187 (LJ14) 9 18 72: 40 type=197 (LJ14) 9 22 72: 41 type=193 (LJ14) 10 13 72: 42 type=193 (LJ14) 10 14 72: 43 type=191 (LJ14) 10 15 72: 44 type=193 (LJ14) 11 13 72: 45 type=193 (LJ14) 11 14 72: 46 type=191 (LJ14) 11 15 72: 47 type=190 (LJ14) 12 19 72: 48 type=190 (LJ14) 12 20 72: 49 type=190 (LJ14) 12 21 72: 50 type=193 (LJ14) 13 16 72: 51 type=193 (LJ14) 13 17 72: 52 type=186 (LJ14) 13 18 72: 53 type=193 (LJ14) 14 16 72: 54 type=193 (LJ14) 14 17 72: 55 type=186 (LJ14) 14 18 72: 56 type=190 (LJ14) 16 19 72: 57 type=190 (LJ14) 16 20 72: 58 type=190 (LJ14) 16 21 72: 59 type=190 (LJ14) 17 19 72: 60 type=190 (LJ14) 17 20 72: 61 type=190 (LJ14) 17 21 72: 62 type=196 (LJ14) 22 27 72: 63 type=197 (LJ14) 22 28 72: 64 type=198 (LJ14) 22 38 72: 65 type=190 (LJ14) 23 25 72: 66 type=195 (LJ14) 23 26 72: 67 type=186 (LJ14) 24 29 72: 68 type=187 (LJ14) 24 30 72: 69 type=187 (LJ14) 24 34 72: 70 type=188 (LJ14) 24 39 72: 71 type=189 (LJ14) 24 40 72: 72 type=190 (LJ14) 25 27 72: 73 type=190 (LJ14) 25 28 72: 74 type=190 (LJ14) 25 38 72: 75 type=191 (LJ14) 26 31 72: 76 type=191 (LJ14) 26 32 72: 77 type=191 (LJ14) 26 33 72: 78 type=191 (LJ14) 26 35 72: 79 type=191 (LJ14) 26 36 72: 80 type=191 (LJ14) 26 37 72: 81 type=190 (LJ14) 26 41 72: 82 type=192 (LJ14) 26 42 72: 83 type=193 (LJ14) 27 29 72: 84 type=191 (LJ14) 27 30 72: 85 type=191 (LJ14) 27 34 72: 86 type=194 (LJ14) 27 39 72: 87 type=186 (LJ14) 27 40 72: 88 type=195 (LJ14) 28 39 72: 89 type=187 (LJ14) 28 40 72: 90 type=193 (LJ14) 29 31 72: 91 type=193 (LJ14) 29 32 72: 92 type=193 (LJ14) 29 33 72: 93 type=193 (LJ14) 29 35 72: 94 type=193 (LJ14) 29 36 72: 95 type=193 (LJ14) 29 37 72: 96 type=196 (LJ14) 29 38 72: 97 type=191 (LJ14) 30 35 72: 98 type=191 (LJ14) 30 36 72: 99 type=191 (LJ14) 30 37 72: 100 type=197 (LJ14) 30 38 72: 101 type=191 (LJ14) 31 34 72: 102 type=191 (LJ14) 32 34 72: 103 type=191 (LJ14) 33 34 72: 104 type=197 (LJ14) 34 38 72: 105 type=196 (LJ14) 38 43 72: 106 type=197 (LJ14) 38 44 72: 107 type=198 (LJ14) 38 58 72: 108 type=190 (LJ14) 39 41 72: 109 type=195 (LJ14) 39 42 72: 110 type=186 (LJ14) 40 45 72: 111 type=186 (LJ14) 40 46 72: 112 type=199 (LJ14) 40 47 72: 113 type=188 (LJ14) 40 59 72: 114 type=189 (LJ14) 40 60 72: 115 type=190 (LJ14) 41 43 72: 116 type=190 (LJ14) 41 44 72: 117 type=190 (LJ14) 41 58 72: 118 type=200 (LJ14) 42 48 72: 119 type=200 (LJ14) 42 50 72: 120 type=190 (LJ14) 42 61 72: 121 type=192 (LJ14) 42 62 72: 122 type=193 (LJ14) 43 45 72: 123 type=193 (LJ14) 43 46 72: 124 type=201 (LJ14) 43 47 72: 125 type=194 (LJ14) 43 59 72: 126 type=186 (LJ14) 43 60 72: 127 type=202 (LJ14) 44 49 72: 128 type=202 (LJ14) 44 51 72: 129 type=200 (LJ14) 44 52 72: 130 type=200 (LJ14) 44 54 72: 131 type=195 (LJ14) 44 59 72: 132 type=187 (LJ14) 44 60 72: 133 type=201 (LJ14) 45 48 72: 134 type=201 (LJ14) 45 50 72: 135 type=196 (LJ14) 45 58 72: 136 type=201 (LJ14) 46 48 72: 137 type=201 (LJ14) 46 50 72: 138 type=196 (LJ14) 46 58 72: 139 type=203 (LJ14) 47 53 72: 140 type=203 (LJ14) 47 55 72: 141 type=204 (LJ14) 47 56 72: 142 type=205 (LJ14) 47 58 72: 143 type=203 (LJ14) 48 51 72: 144 type=204 (LJ14) 48 54 72: 145 type=203 (LJ14) 48 57 72: 146 type=203 (LJ14) 49 50 72: 147 type=206 (LJ14) 49 53 72: 148 type=203 (LJ14) 49 56 72: 149 type=204 (LJ14) 50 52 72: 150 type=203 (LJ14) 50 57 72: 151 type=206 (LJ14) 51 55 72: 152 type=203 (LJ14) 51 56 72: 153 type=203 (LJ14) 52 55 72: 154 type=203 (LJ14) 53 54 72: 155 type=206 (LJ14) 53 57 72: 156 type=206 (LJ14) 55 57 72: 157 type=196 (LJ14) 58 63 72: 158 type=196 (LJ14) 58 64 72: 159 type=198 (LJ14) 58 65 72: 160 type=190 (LJ14) 59 61 72: 161 type=195 (LJ14) 59 62 72: 162 type=188 (LJ14) 60 66 72: 163 type=189 (LJ14) 60 67 72: 164 type=190 (LJ14) 61 63 72: 165 type=190 (LJ14) 61 64 72: 166 type=190 (LJ14) 61 65 72: 167 type=190 (LJ14) 62 68 72: 168 type=192 (LJ14) 62 69 72: 169 type=194 (LJ14) 63 66 72: 170 type=186 (LJ14) 63 67 72: 171 type=194 (LJ14) 64 66 72: 172 type=186 (LJ14) 64 67 72: 173 type=196 (LJ14) 65 70 72: 174 type=197 (LJ14) 65 71 72: 175 type=198 (LJ14) 65 89 72: 176 type=190 (LJ14) 66 68 72: 177 type=195 (LJ14) 66 69 72: 178 type=186 (LJ14) 67 72 72: 179 type=186 (LJ14) 67 73 72: 180 type=187 (LJ14) 67 74 72: 181 type=188 (LJ14) 67 90 72: 182 type=189 (LJ14) 67 91 72: 183 type=190 (LJ14) 68 70 72: 184 type=190 (LJ14) 68 71 72: 185 type=190 (LJ14) 68 89 72: 186 type=191 (LJ14) 69 75 72: 187 type=191 (LJ14) 69 76 72: 188 type=192 (LJ14) 69 77 72: 189 type=190 (LJ14) 69 92 72: 190 type=192 (LJ14) 69 93 72: 191 type=193 (LJ14) 70 72 72: 192 type=193 (LJ14) 70 73 72: 193 type=191 (LJ14) 70 74 72: 194 type=194 (LJ14) 70 90 72: 195 type=186 (LJ14) 70 91 72: 196 type=191 (LJ14) 71 78 72: 197 type=191 (LJ14) 71 79 72: 198 type=187 (LJ14) 71 80 72: 199 type=195 (LJ14) 71 90 72: 200 type=187 (LJ14) 71 91 72: 201 type=193 (LJ14) 72 75 72: 202 type=193 (LJ14) 72 76 72: 203 type=191 (LJ14) 72 77 72: 204 type=196 (LJ14) 72 89 72: 205 type=193 (LJ14) 73 75 72: 206 type=193 (LJ14) 73 76 72: 207 type=191 (LJ14) 73 77 72: 208 type=196 (LJ14) 73 89 72: 209 type=190 (LJ14) 74 81 72: 210 type=207 (LJ14) 74 82 72: 211 type=197 (LJ14) 74 89 72: 212 type=193 (LJ14) 75 78 72: 213 type=193 (LJ14) 75 79 72: 214 type=186 (LJ14) 75 80 72: 215 type=193 (LJ14) 76 78 72: 216 type=193 (LJ14) 76 79 72: 217 type=186 (LJ14) 76 80 72: 218 type=187 (LJ14) 77 83 72: 219 type=187 (LJ14) 77 86 72: 220 type=190 (LJ14) 78 81 72: 221 type=208 (LJ14) 78 82 72: 222 type=190 (LJ14) 79 81 72: 223 type=208 (LJ14) 79 82 72: 224 type=190 (LJ14) 80 84 72: 225 type=190 (LJ14) 80 85 72: 226 type=190 (LJ14) 80 87 72: 227 type=190 (LJ14) 80 88 72: 228 type=190 (LJ14) 81 83 72: 229 type=190 (LJ14) 81 86 72: 230 type=190 (LJ14) 83 87 72: 231 type=190 (LJ14) 83 88 72: 232 type=190 (LJ14) 84 86 72: 233 type=190 (LJ14) 85 86 72: 234 type=196 (LJ14) 89 94 72: 235 type=197 (LJ14) 89 95 72: 236 type=198 (LJ14) 89 100 72: 237 type=190 (LJ14) 90 92 72: 238 type=195 (LJ14) 90 93 72: 239 type=186 (LJ14) 91 96 72: 240 type=186 (LJ14) 91 97 72: 241 type=209 (LJ14) 91 98 72: 242 type=188 (LJ14) 91 101 72: 243 type=189 (LJ14) 91 102 72: 244 type=190 (LJ14) 92 94 72: 245 type=190 (LJ14) 92 95 72: 246 type=190 (LJ14) 92 100 72: 247 type=190 (LJ14) 93 99 72: 248 type=190 (LJ14) 93 103 72: 249 type=192 (LJ14) 93 104 72: 250 type=193 (LJ14) 94 96 72: 251 type=193 (LJ14) 94 97 72: 252 type=210 (LJ14) 94 98 72: 253 type=194 (LJ14) 94 101 72: 254 type=186 (LJ14) 94 102 72: 255 type=195 (LJ14) 95 101 72: 256 type=187 (LJ14) 95 102 72: 257 type=190 (LJ14) 96 99 72: 258 type=196 (LJ14) 96 100 72: 259 type=190 (LJ14) 97 99 72: 260 type=196 (LJ14) 97 100 72: 261 type=211 (LJ14) 98 100 72: 262 type=196 (LJ14) 100 105 72: 263 type=197 (LJ14) 100 106 72: 264 type=198 (LJ14) 100 115 72: 265 type=190 (LJ14) 101 103 72: 266 type=195 (LJ14) 101 104 72: 267 type=186 (LJ14) 102 107 72: 268 type=186 (LJ14) 102 108 72: 269 type=187 (LJ14) 102 109 72: 270 type=188 (LJ14) 102 116 72: 271 type=189 (LJ14) 102 117 72: 272 type=190 (LJ14) 103 105 72: 273 type=190 (LJ14) 103 106 72: 274 type=190 (LJ14) 103 115 72: 275 type=191 (LJ14) 104 110 72: 276 type=191 (LJ14) 104 111 72: 277 type=197 (LJ14) 104 112 72: 278 type=190 (LJ14) 104 118 72: 279 type=192 (LJ14) 104 119 72: 280 type=193 (LJ14) 105 107 72: 281 type=193 (LJ14) 105 108 72: 282 type=191 (LJ14) 105 109 72: 283 type=194 (LJ14) 105 116 72: 284 type=186 (LJ14) 105 117 72: 285 type=195 (LJ14) 106 113 72: 286 type=195 (LJ14) 106 114 72: 287 type=195 (LJ14) 106 116 72: 288 type=187 (LJ14) 106 117 72: 289 type=193 (LJ14) 107 110 72: 290 type=193 (LJ14) 107 111 72: 291 type=196 (LJ14) 107 112 72: 292 type=196 (LJ14) 107 115 72: 293 type=193 (LJ14) 108 110 72: 294 type=193 (LJ14) 108 111 72: 295 type=196 (LJ14) 108 112 72: 296 type=196 (LJ14) 108 115 72: 297 type=197 (LJ14) 109 115 72: 298 type=194 (LJ14) 110 113 72: 299 type=194 (LJ14) 110 114 72: 300 type=194 (LJ14) 111 113 72: 301 type=194 (LJ14) 111 114 72: 302 type=196 (LJ14) 115 120 72: 303 type=197 (LJ14) 115 121 72: 304 type=198 (LJ14) 115 134 72: 305 type=190 (LJ14) 116 118 72: 306 type=195 (LJ14) 116 119 72: 307 type=186 (LJ14) 117 122 72: 308 type=186 (LJ14) 117 123 72: 309 type=187 (LJ14) 117 124 72: 310 type=188 (LJ14) 117 135 72: 311 type=189 (LJ14) 117 136 72: 312 type=190 (LJ14) 118 120 72: 313 type=190 (LJ14) 118 121 72: 314 type=190 (LJ14) 118 134 72: 315 type=191 (LJ14) 119 125 72: 316 type=192 (LJ14) 119 126 72: 317 type=192 (LJ14) 119 130 72: 318 type=190 (LJ14) 119 137 72: 319 type=192 (LJ14) 119 138 72: 320 type=193 (LJ14) 120 122 72: 321 type=193 (LJ14) 120 123 72: 322 type=191 (LJ14) 120 124 72: 323 type=194 (LJ14) 120 135 72: 324 type=186 (LJ14) 120 136 72: 325 type=191 (LJ14) 121 127 72: 326 type=191 (LJ14) 121 128 72: 327 type=191 (LJ14) 121 129 72: 328 type=191 (LJ14) 121 131 72: 329 type=191 (LJ14) 121 132 72: 330 type=191 (LJ14) 121 133 72: 331 type=195 (LJ14) 121 135 72: 332 type=187 (LJ14) 121 136 72: 333 type=193 (LJ14) 122 125 72: 334 type=191 (LJ14) 122 126 72: 335 type=191 (LJ14) 122 130 72: 336 type=196 (LJ14) 122 134 72: 337 type=193 (LJ14) 123 125 72: 338 type=191 (LJ14) 123 126 72: 339 type=191 (LJ14) 123 130 72: 340 type=196 (LJ14) 123 134 72: 341 type=197 (LJ14) 124 134 72: 342 type=193 (LJ14) 125 127 72: 343 type=193 (LJ14) 125 128 72: 344 type=193 (LJ14) 125 129 72: 345 type=193 (LJ14) 125 131 72: 346 type=193 (LJ14) 125 132 72: 347 type=193 (LJ14) 125 133 72: 348 type=191 (LJ14) 126 131 72: 349 type=191 (LJ14) 126 132 72: 350 type=191 (LJ14) 126 133 72: 351 type=191 (LJ14) 127 130 72: 352 type=191 (LJ14) 128 130 72: 353 type=191 (LJ14) 129 130 72: 354 type=196 (LJ14) 134 139 72: 355 type=197 (LJ14) 134 140 72: 356 type=198 (LJ14) 134 144 72: 357 type=190 (LJ14) 135 137 72: 358 type=195 (LJ14) 135 138 72: 359 type=186 (LJ14) 136 141 72: 360 type=186 (LJ14) 136 142 72: 361 type=186 (LJ14) 136 143 72: 362 type=188 (LJ14) 136 145 72: 363 type=189 (LJ14) 136 146 72: 364 type=190 (LJ14) 137 139 72: 365 type=190 (LJ14) 137 140 72: 366 type=190 (LJ14) 137 144 72: 367 type=190 (LJ14) 138 147 72: 368 type=192 (LJ14) 138 148 72: 369 type=193 (LJ14) 139 141 72: 370 type=193 (LJ14) 139 142 72: 371 type=193 (LJ14) 139 143 72: 372 type=194 (LJ14) 139 145 72: 373 type=186 (LJ14) 139 146 72: 374 type=195 (LJ14) 140 145 72: 375 type=187 (LJ14) 140 146 72: 376 type=196 (LJ14) 141 144 72: 377 type=196 (LJ14) 142 144 72: 378 type=196 (LJ14) 143 144 72: 379 type=196 (LJ14) 144 149 72: 380 type=197 (LJ14) 144 150 72: 381 type=198 (LJ14) 144 154 72: 382 type=190 (LJ14) 145 147 72: 383 type=195 (LJ14) 145 148 72: 384 type=186 (LJ14) 146 151 72: 385 type=186 (LJ14) 146 152 72: 386 type=186 (LJ14) 146 153 72: 387 type=188 (LJ14) 146 155 72: 388 type=190 (LJ14) 147 149 72: 389 type=190 (LJ14) 147 150 72: 390 type=190 (LJ14) 147 154 72: 391 type=193 (LJ14) 149 151 72: 392 type=193 (LJ14) 149 152 72: 393 type=193 (LJ14) 149 153 72: 394 type=194 (LJ14) 149 155 72: 395 type=195 (LJ14) 150 155 72: 396 type=196 (LJ14) 151 154 72: 397 type=196 (LJ14) 152 154 72: 398 type=196 (LJ14) 153 154 72: Coulomb-14: 72: nr: 0 72: LJC-14 q: 72: nr: 0 72: LJC Pairs NB: 72: nr: 0 72: LJ (SR): 72: nr: 0 72: Buck.ham (SR): 72: nr: 0 72: LJ: 72: nr: 0 72: B.ham: 72: nr: 0 72: Disper. corr.: 72: nr: 0 72: Coulomb (SR): 72: nr: 0 72: Coul: 72: nr: 0 72: RF excl.: 72: nr: 0 72: Coul. recip.: 72: nr: 0 72: LJ recip.: 72: nr: 0 72: DPD: 72: nr: 0 72: Polarization: 72: nr: 0 72: Water Pol.: 72: nr: 0 72: Thole Pol.: 72: nr: 0 72: Anharm. Pol.: 72: nr: 0 72: Position Rest.: 72: nr: 0 72: Flat-b. P-R.: 72: nr: 0 72: Dis. Rest.: 72: nr: 0 72: D.R.Viol. (nm): 72: nr: 0 72: Orient. Rest.: 72: nr: 0 72: Ori. R. RMSD: 72: nr: 0 72: Angle Rest.: 72: nr: 0 72: Angle Rest. Z: 72: nr: 0 72: Dih. Rest.: 72: nr: 0 72: Dih. Rest. Vi.: 72: nr: 0 72: Constraint: 72: nr: 0 72: Constr. No Co.: 72: nr: 0 72: Settle: 72: nr: 0 72: Virtual site 1: 72: nr: 0 72: Virtual site 2: 72: nr: 0 72: Virt. site 2fd: 72: nr: 0 72: Virtual site 3: 72: nr: 0 72: Virt. site 3fd: 72: nr: 0 72: Vir. site 3fad: 72: nr: 0 72: Vir. site 3out: 72: nr: 0 72: Virt. site 4fd: 72: nr: 0 72: Vir. site 4fdn: 72: nr: 0 72: Virtual site N: 72: nr: 0 72: COM Pull En.: 72: nr: 0 72: Dens. fitting: 72: nr: 0 72: Quantum En.: 72: nr: 0 72: NN Potential: 72: nr: 0 72: Potential: 72: nr: 0 72: Kinetic En.: 72: nr: 0 72: Total Energy: 72: nr: 0 72: Conserved En.: 72: nr: 0 72: Temperature: 72: nr: 0 72: Vir. Temp.: 72: nr: 0 72: Pres. DC: 72: nr: 0 72: Pressure: 72: nr: 0 72: dH/dl constr.: 72: nr: 0 72: dVremain/dl: 72: nr: 0 72: dEkin/dl: 72: nr: 0 72: dVcoul/dl: 72: nr: 0 72: dVvdw/dl: 72: nr: 0 72: dVbonded/dl: 72: nr: 0 72: dVrestraint/dl: 72: nr: 0 72: dVtemp/dl: 72: nr: 0 72: grp[T-Coupling ] nr=1, name=[ rest] 72: grp[Energy Mon. ] nr=1, name=[ rest] 72: grp[Acc. not used] nr=1, name=[ rest] 72: grp[Freeze ] nr=1, name=[ rest] 72: grp[User1 ] nr=1, name=[ rest] 72: grp[User2 ] nr=1, name=[ rest] 72: grp[VCM ] nr=1, name=[ rest] 72: grp[Compressed X] nr=1, name=[ rest] 72: grp[Or. Res. Fit] nr=1, name=[ rest] 72: grp[QMMM ] nr=1, name=[ rest] 72: grpname (11): 72: grpname[0]={name="System"} 72: grpname[1]={name="Protein"} 72: grpname[2]={name="Protein-H"} 72: grpname[3]={name="C-alpha"} 72: grpname[4]={name="Backbone"} 72: grpname[5]={name="MainChain"} 72: grpname[6]={name="MainChain+Cb"} 72: grpname[7]={name="MainChain+H"} 72: grpname[8]={name="SideChain"} 72: grpname[9]={name="SideChain-H"} 72: grpname[10]={name="rest"} 72: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 72: allocated 0 0 0 0 0 0 0 0 0 0 72: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 72: box (3x3): 72: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 72: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 72: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 72: box_rel (3x3): 72: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv (3x3): 72: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev (3x3): 72: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev (3x3): 72: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev (3x3): 72: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: nosehoover_xi: not available 72: x (156x3): 72: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 72: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 72: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 72: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 72: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 72: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 72: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 72: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 72: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 72: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 72: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 72: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 72: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 72: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 72: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 72: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 72: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 72: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 72: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 72: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 72: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 72: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 72: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 72: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 72: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 72: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 72: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 72: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 72: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 72: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 72: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 72: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 72: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 72: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 72: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 72: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 72: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 72: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 72: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 72: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 72: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 72: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 72: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 72: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 72: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 72: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 72: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 72: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 72: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 72: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 72: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 72: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 72: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 72: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 72: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 72: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 72: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 72: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 72: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 72: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 72: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 72: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 72: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 72: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 72: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 72: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 72: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 72: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 72: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 72: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 72: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 72: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 72: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 72: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 72: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 72: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 72: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 72: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 72: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 72: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 72: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 72: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 72: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 72: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 72: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 72: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 72: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 72: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 72: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 72: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 72: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 72: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 72: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 72: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 72: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 72: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 72: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 72: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 72: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 72: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 72: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 72: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 72: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 72: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 72: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 72: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 72: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 72: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 72: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 72: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 72: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 72: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 72: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 72: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 72: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 72: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 72: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 72: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 72: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 72: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 72: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 72: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 72: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 72: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 72: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 72: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 72: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 72: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 72: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 72: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 72: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 72: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 72: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 72: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 72: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 72: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 72: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 72: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 72: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 72: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 72: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 72: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 72: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 72: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 72: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 72: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 72: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 72: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 72: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 72: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 72: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 72: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 72: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 72: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 72: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 72: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 72: v (156x3): 72: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: Group statistics 72: T-Coupling : 156 (total 156 atoms) 72: Energy Mon. : 156 (total 156 atoms) 72: Acc. not used: 156 (total 156 atoms) 72: Freeze : 156 (total 156 atoms) 72: User1 : 156 (total 156 atoms) 72: User2 : 156 (total 156 atoms) 72: VCM : 156 (total 156 atoms) 72: Compressed X: 156 (total 156 atoms) 72: Or. Res. Fit: 156 (total 156 atoms) 72: QMMM : 156 (total 156 atoms) 72: [ OK ] DumpTest.WorksWithTpr (3 ms) 72: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 72: [----------] 2 tests from DumpTest (3 ms total) 72: 72: [----------] 3 tests from HelpwritingTest 72: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 72: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 72: [ RUN ] HelpwritingTest.DumpWritesHelp 72: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 72: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 72: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 72: [----------] 3 tests from HelpwritingTest (0 ms total) 72: 72: [----------] 7 tests from GmxMakeNdx 72: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 16 Protein residues 72: Analysing Protein... 72: 72: 0 System : 256 atoms 72: 1 Protein : 256 atoms 72: 2 Protein-H : 139 atoms 72: 3 C-alpha : 16 atoms 72: 4 Backbone : 48 atoms 72: 5 MainChain : 63 atoms 72: 6 MainChain+Cb : 78 atoms 72: 7 MainChain+H : 81 atoms 72: 8 SideChain : 175 atoms 72: 9 SideChain-H : 76 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (1 ms) 72: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 1 'Protein' 72: Copied index group 2 'Protein-H' 72: Merged two groups with OR: 22 10 -> 22 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 72: [ RUN ] GmxMakeNdx.HandlesNotProtein 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 4 'Backbone' 72: Copied index group 8 'SideChain' 72: Merged two groups with AND: 5 13 -> 0 72: Group is empty 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Removed group 0 'System' 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 72: [ RUN ] GmxMakeNdx.Splitres 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into residues 72: 72: > 72: [ OK ] GmxMakeNdx.Splitres (0 ms) 72: [ RUN ] GmxMakeNdx.Splitat 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into atoms 72: 72: > 72: [ OK ] GmxMakeNdx.Splitat (0 ms) 72: [----------] 7 tests from GmxMakeNdx (4 ms total) 72: 72: [----------] 4 tests from ReportMethodsTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -1411391949 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectInformation 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 72: [ RUN ] ReportMethodsTest.ToolEndToEndTest 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: section: Methods 72: subsection: Simulation system 72: A system of 1 molecules (156 atoms) was simulated. 72: 72: subsection: Simulation settings 72: A total of 0 ns were simulated with a time step of 1 fs. 72: Neighbor searching was performed every 10 steps. 72: The Cut-off algorithm was used for electrostatic interactions. 72: with a cut-off of 1 nm. 72: A single cut-off of 1.1 nm was used for Van der Waals interactions. 72: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 72: [----------] 4 tests from ReportMethodsTest (0 ms total) 72: 72: [----------] 4 tests from ConvertTprTest 72: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Setting the LD random seed to -67510659 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 200000 72: Runtime for the run 200 ps 72: Run end step 200000 72: Run end time 200 ps 72: 72: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (207 ms) 72: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Setting the LD random seed to -1084583042 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime to 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (210 ms) 72: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Setting nsteps to 102 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Setting the LD random seed to -75530497 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 102 72: Runtime for the run 0.102 ps 72: Run end step 102 72: Run end time 0.102 ps 72: 72: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (227 ms) 72: [ RUN ] ConvertTprTest.generateVelocitiesTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Setting the LD random seed to 402480125 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprTest.generateVelocitiesTest (217 ms) 72: [----------] 4 tests from ConvertTprTest (863 ms total) 72: 72: [----------] 1 test from ConvertTprNoVelocityTest 72: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: 72: NOTE 3 [file lysozyme.top, line 1465]: 72: Zero-step energy minimization will alter the coordinates before 72: calculating the energy. If you just want the energy of a single point, 72: try zero-step MD (with unconstrained_start = yes). To do multiple 72: single-point energy evaluations of different configurations of the same 72: topology, use mdrun -rerun. 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 72: Setting the LD random seed to -134653065 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (218 ms) 72: [----------] 1 test from ConvertTprNoVelocityTest (218 ms total) 72: 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: trr version: GMX_trn_file (single precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:86: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:123: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md (0 ms) 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats (6 ms total) 72: 72: [----------] 35 tests from Works/TrjconvDumpTest 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 (0 ms) 72: [----------] 35 tests from Works/TrjconvDumpTest (11 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 70 tests from 8 test suites ran. (1536 ms total) 72: [ PASSED ] 63 tests. 72: [ SKIPPED ] 7 tests, listed below: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72/104 Test #72: ToolUnitTests ............................. Passed 1.55 sec test 73 Start 73: ToolWithLeaksUnitTests 73: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests 73: Test timeout computed to be: 1920 73: [==========] Running 2 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 1 test from ConvertTprTest 73: [ RUN ] ConvertTprTest.selectIndexTest 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 73: Setting the LD random seed to -1140933515 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprTest.selectIndexTest (230 ms) 73: [----------] 1 test from ConvertTprTest (230 ms total) 73: 73: [----------] 1 test from ConvertTprNoVelocityTest 73: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: 73: NOTE 3 [file lysozyme.top, line 1465]: 73: Zero-step energy minimization will alter the coordinates before 73: calculating the energy. If you just want the energy of a single point, 73: try zero-step MD (with unconstrained_start = yes). To do multiple 73: single-point energy evaluations of different configurations of the same 73: topology, use mdrun -rerun. 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 73: Setting the LD random seed to -1074022917 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (217 ms) 73: [----------] 1 test from ConvertTprNoVelocityTest (217 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 2 tests from 2 test suites ran. (448 ms total) 73: [ PASSED ] 2 tests. 73/104 Test #73: ToolWithLeaksUnitTests .................... Passed 0.46 sec test 74 Start 74: H5mdTests 74: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/h5md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/H5mdTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/h5md/tests 74: Test timeout computed to be: 30 74: [==========] Running 1 test from 1 test suite. 74: [----------] Global test environment set-up. 74: [----------] 1 test from H5mdDisabledTest 74: [ RUN ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled 74: [ OK ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled (0 ms) 74: [----------] 1 test from H5mdDisabledTest (0 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 1 test from 1 test suite ran. (0 ms total) 74: [ PASSED ] 1 test. 74/104 Test #74: H5mdTests ................................. Passed 0.01 sec test 75 Start 75: FileIOTests 75: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/FileIOTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/fileio/tests 75: Test timeout computed to be: 30 75: [==========] Running 432 tests from 17 test suites. 75: [----------] Global test environment set-up. 75: [----------] 4 tests from Checkpoint 75: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 75: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 75: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 75: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripInt64 75: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripReal 75: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 75: [----------] 4 tests from Checkpoint (0 ms total) 75: 75: [----------] 1 test from StructureIOTest 75: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 75: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 75: [----------] 1 test from StructureIOTest (0 ms total) 75: 75: [----------] 2 tests from FileMD5Test 75: [ RUN ] FileMD5Test.CanComputeMD5 75: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 75: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 75: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 75: [----------] 2 tests from FileMD5Test (1 ms total) 75: 75: [----------] 4 tests from FileTypeTest 75: [ RUN ] FileTypeTest.CorrectValueForEmptyString 75: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForNoExtension 75: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 75: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 75: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 75: [----------] 4 tests from FileTypeTest (0 ms total) 75: 75: [----------] 4 tests from ColorMapTest 75: [ RUN ] ColorMapTest.CanReadFromFile 75: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 75: [ RUN ] ColorMapTest.CanWriteToFile 75: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 75: [ RUN ] ColorMapTest.RoundTrip 75: [ OK ] ColorMapTest.RoundTrip (0 ms) 75: [ RUN ] ColorMapTest.SearchWorks 75: [ OK ] ColorMapTest.SearchWorks (0 ms) 75: [----------] 4 tests from ColorMapTest (0 ms total) 75: 75: [----------] 4 tests from MatioTest 75: [ RUN ] MatioTest.CanWriteToFile 75: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 75: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanConvertToNewRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 75: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) 75: [----------] 4 tests from MatioTest (1 ms total) 75: 75: [----------] 3 tests from MrcSerializer 75: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 75: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 75: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 75: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 75: [----------] 3 tests from MrcSerializer (0 ms total) 75: 75: [----------] 4 tests from MrcDensityMap 75: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 75: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 75: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 75: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 75: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 75: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 75: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 75: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 75: [----------] 4 tests from MrcDensityMap (0 ms total) 75: 75: [----------] 8 tests from MrcDensityMapHeaderTest 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 75: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.IsSane 75: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 75: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 75: 75: [----------] 10 tests from ReadTest 75: [ RUN ] ReadTest.get_eint_ReadsInteger 75: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_eint64_ReadsInteger 75: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsInteger 75: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsFloat 75: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 75: [ RUN ] ReadTest.get_ereal_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not a 75: real value 75: 75: 75: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 75: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 75: [----------] 10 tests from ReadTest (0 ms total) 75: 75: [----------] 3 tests from TimeControlTest 75: [ RUN ] TimeControlTest.UnSetHasNoValue 75: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 75: [ RUN ] TimeControlTest.CanSetValue 75: [ OK ] TimeControlTest.CanSetValue (0 ms) 75: [ RUN ] TimeControlTest.CanUnsetValueAgain 75: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 75: [----------] 3 tests from TimeControlTest (0 ms total) 75: 75: [----------] 1 test from TngTest 75: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 75: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 75: [----------] 1 test from TngTest (0 ms total) 75: 75: [----------] 4 tests from XvgioTest 75: [ RUN ] XvgioTest.readXvgIntWorks 75: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgRealWorks 75: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 75: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgDeprecatedWorks 75: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 75: [----------] 4 tests from XvgioTest (0 ms total) 75: 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 75: 75: [----------] 370 tests from FileTypeMatch/FileTypeTest 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 (0 ms) 75: [----------] 370 tests from FileTypeMatch/FileTypeTest (6 ms total) 75: 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 (0 ms) 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 (0 ms) 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest (0 ms total) 75: 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 432 tests from 17 test suites ran. (13 ms total) 75: [ PASSED ] 432 tests. 75/104 Test #75: FileIOTests ............................... Passed 0.03 sec test 76 Start 76: SelectionUnitTests 76: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/SelectionUnitTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/gromacs/selection/tests 76: Test timeout computed to be: 30 76: [==========] Running 201 tests from 11 test suites. 76: [----------] Global test environment set-up. 76: [----------] 1 test from IndexGroupTest 76: [ RUN ] IndexGroupTest.RemovesDuplicates 76: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 76: [----------] 1 test from IndexGroupTest (0 ms total) 76: 76: [----------] 15 tests from IndexBlockTest 76: [ RUN ] IndexBlockTest.CreatesUnknownBlock 76: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 76: [ RUN ] IndexBlockTest.CreatesAtomBlock 76: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesSingleBlock 76: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 76: [----------] 15 tests from IndexBlockTest (0 ms total) 76: 76: [----------] 11 tests from IndexMapTest 76: [ RUN ] IndexMapTest.InitializesAtomBlock 76: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 76: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 76: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 76: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 76: [ RUN ] IndexMapTest.InitializesMoleculeBlock 76: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsSingleBlock 76: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocks 76: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 76: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 76: [ RUN ] IndexMapTest.HandlesMultipleRequests 76: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 76: [----------] 11 tests from IndexMapTest (1 ms total) 76: 76: [----------] 3 tests from IndexGroupsAndNamesTest 76: [ RUN ] IndexGroupsAndNamesTest.containsNames 76: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 76: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 76: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 76: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 76: 76: [----------] 15 tests from NeighborhoodSearchTest 76: [ RUN ] NeighborhoodSearchTest.SimpleSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSearch (9 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 76: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (9 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchBox 76: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 76: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (5 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 76: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 76: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 76: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (22 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 76: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 76: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 76: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 76: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 76: [----------] 15 tests from NeighborhoodSearchTest (55 ms total) 76: 76: [----------] 13 tests from PositionCalculationTest 76: [ RUN ] PositionCalculationTest.ComputesAtomPositions 76: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 76: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionMask 76: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 76: [----------] 13 tests from PositionCalculationTest (1 ms total) 76: 76: [----------] 33 tests from SelectionCollectionTest 76: [ RUN ] SelectionCollectionTest.HandlesNoSelections 76: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 76: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 76: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 76: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 76: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 76: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 76: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 76: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 76: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 76: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 76: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 76: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 76: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 76: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 76: [----------] 33 tests from SelectionCollectionTest (5 ms total) 76: 76: [----------] 14 tests from SelectionCollectionInteractiveTest 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 76: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 76: [----------] 14 tests from SelectionCollectionInteractiveTest (2 ms total) 76: 76: [----------] 70 tests from SelectionCollectionDataTest 76: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 76: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 76: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResnr 76: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 76: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 76: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 76: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesChain 76: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMass 76: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCharge 76: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 76: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 76: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 76: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBeta 76: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResname 76: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 76: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 76: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 76: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 76: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 76: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 76: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 76: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 76: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 76: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 76: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 76: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 76: [----------] 70 tests from SelectionCollectionDataTest (30 ms total) 76: 76: [----------] 17 tests from SelectionOptionTest 76: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 76: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 76: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 76: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 76: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptySelections 76: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 76: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelections 76: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 76: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesAdjuster 76: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 76: [----------] 17 tests from SelectionOptionTest (2 ms total) 76: 76: [----------] 9 tests from SelectionFileOptionTest 76: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 76: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 76: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 76: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 201 tests from 11 test suites ran. (103 ms total) 76: [ PASSED ] 201 tests. 76/104 Test #76: SelectionUnitTests ........................ Passed 0.12 sec test 77 Start 77: MdrunOutputTests 77: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunOutputTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 12 tests from 5 test suites. 77: [----------] Global test environment set-up. 77: [----------] 1 test from MdrunTest 77: [ RUN ] MdrunTest.WritesHelp 77: [ OK ] MdrunTest.WritesHelp (15 ms) 77: [----------] 1 test from MdrunTest (15 ms total) 77: 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -1779703818 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.024 0.012 199.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 14.059 1.707 6.145 0.001 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (17 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -1103495973 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.017 0.009 199.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 19.786 1.213 4.367 0.001 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (13 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -403708042 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.016 0.008 199.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 21.434 1.120 4.031 0.001 77: Reading frame 0 time 0.000 77: # Atoms 3 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (12 ms) 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (43 ms total) 77: 77: [----------] 2 tests from Argon12/OutputFiles 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.017 0.009 199.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 168.456 0.142 0.513 0.023 77: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (12 ms) 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.008 199.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 189.498 0.127 0.456 0.026 77: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (12 ms) 77: [----------] 2 tests from Argon12/OutputFiles (25 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/Trajectories 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -134504706 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.018 0.009 199.0 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 65.238 0.368 1.324 0.005 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (14 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -621677185 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.019 0.010 198.7 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 62.249 0.386 1.388 0.004 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (15 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to 489072638 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.014 0.007 198.8 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 85.819 0.280 1.007 0.006 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (14 ms) 77: [----------] 3 tests from MdrunCanWrite/Trajectories (44 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -1216618625 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.006 198.6 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 44.776 0.536 1.930 0.003 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (10 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 77: 77: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: The Berendsen barostat does not generate any strictly correct ensemble, 77: and should not be used for new production simulations (in our opinion). 77: We recommend using the C-rescale barostat instead. 77: 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: 77: There was 1 WARNING 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -152210530 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.006 198.6 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 46.512 0.516 1.858 0.003 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (12 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -25237538 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 198.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 43.976 0.546 1.965 0.003 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (10 ms) 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories (34 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 12 tests from 5 test suites ran. (216 ms total) 77: [ PASSED ] 12 tests. 77/104 Test #77: MdrunOutputTests .......................... Passed 0.23 sec test 78 Start 78: MdrunModulesTests 78: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunModulesTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 15 tests from 3 test suites. 78: [----------] Global test environment set-up. 78: [----------] 9 tests from DensityFittingTest 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.8565254e+03 78: Maximum force = 4.5099883e+03 on atom 3 78: Norm of force = 1.6816849e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1208288515 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (5 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -9.8207725e+03 78: Maximum force = 7.3954834e+03 on atom 2 78: Norm of force = 2.7825089e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1761657234 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (4 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (4 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Overriding nsteps with value passed on the command line: 4 steps 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 4 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 5 steps. 78: Potential Energy = -5.4739302e+03 78: Maximum force = 6.1322041e+03 on atom 2 78: Norm of force = 1.7702155e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -1610619465 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (4 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (4 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.8565254e+03 78: Maximum force = 4.5099883e+03 on atom 3 78: Norm of force = 1.6816849e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -8933378 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (4 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -2.7138664e+04 78: Maximum force = 6.7827656e+03 on atom 2 78: Norm of force = 1.9608866e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -11010313 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (4 ms) 78: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: Setting the LD random seed to -54797828 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 78: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (4 ms) 78: [ RUN ] DensityFittingTest.CheckpointWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (2) 78: 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -1352797505 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.015 0.008 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 33.367 0.719 2.589 0.005 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 78: Can not increase nstlist because an NVE ensemble is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.010 0.005 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 86.279 0.278 1.001 0.012 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (18 ms) 78: [----------] 9 tests from DensityFittingTest (54 ms total) 78: 78: [----------] 4 tests from MimicTest 78: [ RUN ] MimicTest.OneQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 22 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 184.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 579.821 0.041 0.149 0.081 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -8413457 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.OneQuantumMol (4 ms) 78: [ RUN ] MimicTest.AllQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 17 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 183.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 480.621 0.050 0.180 0.067 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1644204237 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.AllQuantumMol (4 ms) 78: [ RUN ] MimicTest.TwoQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 19 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 182.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 586.388 0.041 0.147 0.081 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -289767442 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.TwoQuantumMol (3 ms) 78: [ RUN ] MimicTest.BondCuts 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 66.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: NVE simulation: will use the initial temperature of 300.368 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 78: 78: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 22 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 190.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 381.060 0.063 0.227 0.101 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -579211417 78: 78: Generated 2211 of the 2211 non-bonded parameter combinations 78: 78: Generated 2211 of the 2211 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.BondCuts (9 ms) 78: [----------] 4 tests from MimicTest (21 ms total) 78: 78: [----------] 2 tests from WithIntegrator/ImdTest 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 78: Generating 1-4 interactions: fudge = 1 78: 78: NOTE 1 [file glycine_vacuo.top, line 12]: 78: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 78: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 78: the time step of 2.0e-03 ps. 78: Maybe you forgot to change the constraints mdp option. 78: 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 59393. 78: IMD: -imdwait not set, starting simulation. 78: starting mdrun 'Glycine' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to 1065353087 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.016 0.008 198.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 63.651 0.377 2.715 0.004 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (67 ms) 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 78: apply to steep. 78: 78: Generating 1-4 interactions: fudge = 1 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 53733. 78: IMD: -imdwait not set, starting simulation. 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = 1.1977064e+03 78: Maximum force = 1.7794877e+04 on atom 9 78: Norm of force = 7.8732901e+03 78: Setting the LD random seed to -1661110294 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (58 ms) 78: [----------] 2 tests from WithIntegrator/ImdTest (125 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 15 tests from 3 test suites ran. (244 ms total) 78: [ PASSED ] 15 tests. 78/104 Test #78: MdrunModulesTests ......................... Passed 0.26 sec test 79 Start 79: MdrunIOTests 79: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunIOTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 76 tests from 13 test suites. 79: [----------] Global test environment set-up. 79: [----------] 9 tests from GromppTest 79: [ RUN ] GromppTest.EmptyMdpFileWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -1746141825 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group rest: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -134316297 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group Methanol: Single, 3 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 3.0 280.0 79: 6.0- 270.0 79: Simulated annealing for group SOL: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group Methanol is 7.20 79: Number of degrees of freedom in T-Coupling group SOL is 4.80 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to 1867606015 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 79: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 79: Setting the LD random seed to -268566562 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (4 ms) 79: [ RUN ] GromppTest.HandlesMaxwarn 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: The Berendsen thermostat does not generate the correct kinetic energy 79: distribution, and should not be used for new production simulations (in 79: our opinion). We would recommend the V-rescale thermostat. 79: 79: Number of degrees of freedom in T-Coupling group System is 12.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Setting the LD random seed to -604603477 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 79: [ RUN ] GromppTest.MaxwarnShouldBePositive 79: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 79: [ RUN ] GromppTest.ValidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: 0.613 nm 0.000 nm 79: 79: There were 3 NOTEs 79: Setting the LD random seed to 532152319 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 79: [ RUN ] GromppTest.InvalidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: Setting the LD random seed to -839122978 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: [ OK ] GromppTest.InvalidTransformationCoord (2 ms) 79: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 79: Setting the LD random seed to -1677721729 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (4 ms) 79: [----------] 9 tests from GromppTest (26 ms total) 79: 79: [----------] 6 tests from MdrunTerminationTest 79: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -539295905 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 34.684 0.692 2.491 0.002 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.007 0.003 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.869 0.312 1.124 0.005 79: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (17 ms) 79: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 1.032 to 1 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 8: Run time exceeded 0.000 hours, will terminate the run within 200 steps 79: Setting the LD random seed to 2119941948 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 19 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 1052.393 0.023 0.082 0.073 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 102 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 100 79: Runtime for the run 0.1 ps 79: Run end step 100 79: Run end time 0.1 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 102 79: Runtime for the run 0.102 ps 79: Run end step 102 79: Run end time 0.102 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.007 0.003 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 74.224 0.323 1.164 0.005 79: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (17 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -142610689 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 57.479 0.418 1.503 0.004 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 52.345 0.458 1.651 0.004 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 6 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 53.655 0.447 1.610 0.004 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 8 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 8 79: Runtime for the run 0.008 ps 79: Run end step 8 79: Run end time 0.008 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 49.027 0.490 1.762 0.003 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: NOTE: 24 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.000 175.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 831.165 0.029 0.104 0.058 79: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (32 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -1835073 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 45.770 0.524 1.888 0.003 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 83.265 0.288 1.038 0.006 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (16 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to 2146959343 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 48.037 0.500 1.799 0.003 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 4 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (10 ms) 79: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to 1333590463 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 53.719 0.447 1.608 0.004 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 46.609 0.515 1.854 0.003 79: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (17 ms) 79: [----------] 6 tests from MdrunTerminationTest (112 ms total) 79: 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 186.679 0.129 0.463 0.013 79: trr version: GMX_trn_file (single precision) 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: 79: Dumping frame at t= 0.016 ps 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Last frame -1 time 0.016 79: 79: There were 3 NOTEs 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: Analysing residue names: 79: There are: 2 Water residues 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: Reading Coordinates, Velocities and Box size from old trajectory 79: 79: Will read whole trajectory 79: 79: Using frame at t = 0.016 ps 79: 79: Starting time for run is 0 ps 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (15 ms) 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 185.281 0.130 0.466 0.013 79: 79: 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (11 ms) 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (27 ms total) 79: 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 201.669 0.119 0.428 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.203 0.226 0.814 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.251 0.222 0.798 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 196.491 0.122 0.440 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.638 0.232 0.834 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 114.054 0.210 0.758 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 194.672 0.123 0.444 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 113.195 0.212 0.763 0.016 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.658 0.223 0.803 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 198.370 0.121 0.436 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.338 0.226 0.813 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.315 0.228 0.820 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 192.362 0.125 0.449 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.609 0.243 0.876 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.010 0.229 0.823 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (31 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 178.812 0.134 0.483 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 109.475 0.219 0.789 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 93.522 0.257 0.924 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 180.372 0.133 0.479 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 114.942 0.209 0.752 0.016 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 118.993 0.202 0.726 0.017 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 201.412 0.119 0.429 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.802 0.245 0.883 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.149 0.247 0.889 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.006 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 232.624 0.103 0.371 0.016 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 119.133 0.201 0.725 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.011 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 68.902 0.348 1.254 0.005 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (33 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 158.934 0.151 0.544 0.011 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.505 0.227 0.819 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.319 0.222 0.798 0.008 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 194.059 0.124 0.445 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.931 0.235 0.848 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 99.475 0.241 0.869 0.007 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 203.669 0.118 0.424 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.377 0.221 0.797 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.321 0.224 0.805 0.007 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (31 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 192.922 0.124 0.448 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 92.960 0.258 0.929 0.006 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.346 0.232 0.836 0.007 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.050 0.025 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 58.213 0.412 1.484 0.004 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.297 0.149 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 5.229 4.589 16.522 0.000 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.172 0.086 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.021 2.660 9.577 0.001 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (285 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 185.935 0.129 0.465 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 89.928 0.267 0.961 0.006 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.298 0.222 0.798 0.008 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (34 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 183.482 0.131 0.471 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 81.336 0.295 1.062 0.006 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 109.826 0.219 0.787 0.008 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (34 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 146.999 0.163 0.588 0.049 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.101 0.228 0.822 0.035 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.454 0.244 0.878 0.033 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (48 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 139.642 0.172 0.619 0.047 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.670 0.251 0.903 0.032 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 88.160 0.272 0.980 0.030 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (50 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 153.066 0.157 0.564 0.051 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 99.789 0.241 0.866 0.033 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 102.511 0.234 0.843 0.034 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (48 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 151.084 0.159 0.572 0.051 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 93.223 0.257 0.927 0.031 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.320 0.247 0.888 0.033 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (48 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 154.560 0.155 0.559 0.052 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.043 0.245 0.881 0.033 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.457 0.254 0.915 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (68 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 165.363 0.145 0.522 0.056 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 96.820 0.248 0.892 0.032 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.096 0.252 0.909 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (135 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 148.523 0.162 0.582 0.050 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 89.796 0.267 0.962 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 91.144 0.263 0.948 0.031 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (65 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 152.781 0.157 0.566 0.051 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 96.076 0.250 0.899 0.032 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.287 0.252 0.907 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (81 ms) 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1321 ms total) 79: 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 138.971 0.173 0.622 0.058 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 85.397 0.281 1.012 0.036 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 85.994 0.279 1.005 0.036 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (51 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 138.387 0.173 0.624 0.058 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.009 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 82.685 0.290 1.045 0.034 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 80.568 0.298 1.072 0.034 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (51 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.010 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 141.568 0.170 0.610 0.059 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 81.801 0.293 1.056 0.034 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 78.426 0.306 1.102 0.033 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (52 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 125.860 0.191 0.686 0.052 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 72.523 0.331 1.191 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 81.779 0.293 1.057 0.034 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (53 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 144.608 0.166 0.597 0.060 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.813 0.312 1.125 0.032 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 73.285 0.327 1.179 0.031 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (65 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 137.692 0.174 0.627 0.057 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 72.205 0.332 1.197 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 69.212 0.347 1.248 0.029 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (150 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 127.396 0.188 0.678 0.053 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 72.861 0.329 1.186 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 69.450 0.346 1.244 0.029 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (65 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.010 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 141.486 0.170 0.611 0.059 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 71.855 0.334 1.202 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 77.261 0.311 1.118 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (70 ms) 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (561 ms total) 79: 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 183.166 0.131 0.472 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.481 0.230 0.827 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.404 0.226 0.812 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (32 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 184.681 0.130 0.468 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 102.643 0.234 0.842 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.326 0.247 0.888 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (33 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 180.393 0.133 0.479 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 100.212 0.239 0.862 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.985 0.231 0.831 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (32 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 195.308 0.123 0.442 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 112.330 0.214 0.769 0.016 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.282 0.226 0.813 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (31 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 176.597 0.136 0.489 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.932 0.231 0.831 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 92.611 0.259 0.933 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (34 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 185.935 0.129 0.465 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.742 0.225 0.809 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.289 0.237 0.853 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (32 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 176.102 0.136 0.491 0.024 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.126 0.247 0.890 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 84.661 0.283 1.021 0.012 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (36 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 184.438 0.130 0.468 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 99.185 0.242 0.871 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.888 0.253 0.911 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (33 ms) 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (267 ms total) 79: 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 179.071 0.134 0.482 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.534 0.236 0.851 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 90.741 0.264 0.952 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (33 ms) 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 187.743 0.128 0.460 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.952 0.253 0.910 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 100.418 0.239 0.860 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (33 ms) 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (67 ms total) 79: 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 162.519 0.148 0.532 0.023 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 100.295 0.239 0.861 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.124 0.224 0.807 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (33 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 190.101 0.126 0.454 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.054 0.252 0.909 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.404 0.244 0.878 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (32 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 148.817 0.161 0.581 0.021 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.032 0.224 0.807 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.039 0.233 0.839 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (33 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 205.978 0.117 0.419 0.029 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.843 0.221 0.794 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.652 0.246 0.885 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (31 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 179.264 0.134 0.482 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 85.079 0.282 1.016 0.012 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 109.226 0.220 0.791 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (34 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 203.602 0.118 0.424 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.290 0.232 0.836 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.247 0.228 0.821 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (31 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 172.223 0.139 0.502 0.024 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 109.358 0.219 0.790 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.932 0.243 0.873 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (32 ms) 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (229 ms total) 79: 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 79: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 165.572 0.145 0.522 0.023 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.449 0.237 0.852 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 91.829 0.261 0.941 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (35 ms) 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (35 ms total) 79: 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.013 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 112.891 0.213 0.765 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 66.659 0.360 1.296 0.005 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.013 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 57.739 0.416 1.496 0.004 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (48 ms) 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.013 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.200 0.216 0.777 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.014 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 55.197 0.435 1.565 0.004 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 63.972 0.375 1.351 0.004 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (49 ms) 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (98 ms total) 79: 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Setting the AWH bias MC random seed to 2076178399 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -268473481 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.018 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 83.458 0.288 1.035 0.021 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.015 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 51.229 0.468 1.687 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.013 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 61.752 0.389 1.399 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (75 ms) 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: Setting the AWH bias MC random seed to -281280513 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -285475585 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.015 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.750 0.246 0.884 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.014 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 55.748 0.431 1.550 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 64.220 0.374 1.345 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (71 ms) 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (147 ms total) 79: 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 79: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.010 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 140.106 0.171 0.617 0.058 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 66.270 0.362 1.304 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.038 0.316 1.136 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (65 ms) 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (65 ms total) 79: 79: [----------] 3 tests from Checking/InitialConstraintsTest 79: [ RUN ] Checking/InitialConstraintsTest.Works/0 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to 1417992142 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 31.448 0.763 2.747 0.002 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (9 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/1 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to -1143021617 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 29.302 0.819 2.949 0.002 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (9 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: Integrator method md-vv-avek is implemented primarily for validation 79: purposes; for molecular dynamics, you should probably be using md or 79: md-vv 79: 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to 1599993843 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 34.392 0.698 2.512 0.002 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (8 ms) 79: [----------] 3 tests from Checking/InitialConstraintsTest (28 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 76 tests from 13 test suites ran. (3152 ms total) 79: [ PASSED ] 76 tests. 79/104 Test #79: MdrunIOTests .............................. Passed 3.17 sec test 80 Start 80: MdrunTestsOneRank 80: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 31 tests from 9 test suites. 80: [----------] Global test environment set-up. 80: [----------] 2 tests from AwhTest 80: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.021 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 85.710 0.280 1.008 0.022 80: [ OK ] AwhTest.SingleBiasMultiDimCanRun (35 ms) 80: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.014 199.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 125.539 0.191 0.688 0.032 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 197.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 208.503 0.115 0.414 0.053 80: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (42 ms) 80: [----------] 2 tests from AwhTest (78 ms total) 80: 80: [----------] 1 test from CompelTest 80: [ RUN ] CompelTest.SwapCanRun 80: Generating 1-4 interactions: fudge = 0.5 80: Split0 group 'Ch0' contains 83 atoms. 80: Split1 group 'Ch1' contains 83 atoms. 80: Solvent group 'SOL' contains 11931 atoms. 80: Swap group 'NA+' contains 19 atoms. 80: Swap group 'CL-' contains 19 atoms. 80: Number of degrees of freedom in T-Coupling group System is 27869.00 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Determining initial numbers of ions per compartment. 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 2 steps, 0.0 ps. 80: Setting the LD random seed to -110372633 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning all bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 36 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.168 0.084 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 12.333 1.946 28.023 0.493 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 80: 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Copying channel fluxes from checkpoint file data 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: NOTE: 23 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.119 0.060 199.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 17.390 1.380 19.874 0.695 80: [ OK ] CompelTest.SwapCanRun (437 ms) 80: [----------] 1 test from CompelTest (437 ms total) 80: 80: [----------] 6 tests from BondedInteractionsTest 80: [ RUN ] BondedInteractionsTest.NormalBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 21 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 185.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 465.196 0.052 0.186 0.022 80: Setting the LD random seed to -25176097 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalBondWorks (4 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 20 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 185.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 572.493 0.042 0.151 0.027 80: Setting the LD random seed to -436208265 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedBondWorks (4 ms) 80: [ RUN ] BondedInteractionsTest.NormalAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 19 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 184.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 673.583 0.036 0.128 0.031 80: Setting the LD random seed to -875794455 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalAngleWorks (3 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 17 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 184.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 444.648 0.054 0.194 0.021 80: Setting the LD random seed to -671122813 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (4 ms) 80: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 17 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 174.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 602.975 0.040 0.143 0.028 80: Setting the LD random seed to 782659575 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalDihedralWorks (3 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 18 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 184.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 641.394 0.037 0.135 0.030 80: Setting the LD random seed to 1979446459 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (3 ms) 80: [----------] 6 tests from BondedInteractionsTest (23 ms total) 80: 80: [----------] 2 tests from BoxDeformationTest 80: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 23 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 167.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1228.433 0.020 0.141 0.085 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -31541393 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Setting gen_seed to -103989390 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (4 ms) 80: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group rest is 1293.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 20 steps, 0.0 ps. 80: Setting the LD random seed to -134481093 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 80: 80: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 80: 80: Estimate for the relative computational load of the PME mesh part: 0.20 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.021 199.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 173.605 0.138 0.995 0.651 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (238 ms) 80: [----------] 2 tests from BoxDeformationTest (242 ms total) 80: 80: [----------] 1 test from PositionRestraintCommTest 80: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any of the VCM groups 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any center of mass motion removal group. 80: This may lead to artifacts. 80: In most cases one should use one group for the whole system. 80: 80: Number of degrees of freedom in T-Coupling group System is 29527.73 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Channel_coco in octane membrane' 80: 10 steps, 0.0 ps. 80: Setting the LD random seed to -124010581 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 15 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.185 0.092 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 20.556 1.168 8.406 1.644 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (370 ms) 80: [----------] 1 test from PositionRestraintCommTest (370 ms total) 80: 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 2012471162 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 198.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 40.682 0.590 2.124 0.011 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -274567 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 53.741 0.447 1.608 0.014 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 80: 80: 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (406 ms) 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1080689033 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 54.897 0.437 1.574 0.015 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1043006579 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 54.458 0.441 1.587 0.014 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (37 ms) 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (443 ms total) 80: 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -8559838 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.023 0.012 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 37.491 0.640 2.305 0.003 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -278569 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.011 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 38.186 0.628 2.263 0.003 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (31 ms) 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (31 ms total) 80: 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.007 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 105.318 0.228 0.820 0.027 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (15 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 101.763 0.236 0.849 0.026 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (16 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.008 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 93.428 0.257 0.925 0.024 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (16 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 108.434 0.221 0.797 0.028 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (15 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 101.877 0.236 0.848 0.026 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (15 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 80: Parrinello-Rahman is not implemented in md-vv. 80: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 108.100 0.222 0.799 0.028 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (18 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 103.438 0.232 0.835 0.026 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (18 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 100.098 0.240 0.863 0.025 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (19 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 90.424 0.265 0.956 0.023 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (35 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 99.807 0.240 0.866 0.025 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (33 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 103.316 0.232 0.836 0.026 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (33 ms) 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest (238 ms total) 80: 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -1093051009 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 199.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 189.017 0.127 0.914 0.007 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (12 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -541116681 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 199.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 194.629 0.123 0.888 0.007 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (12 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -13111434 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 199.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 182.901 0.131 0.945 0.006 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (12 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -1140868609 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 199.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 170.786 0.141 1.012 0.006 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (12 ms) 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (50 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 31 tests from 9 test suites ran. (2033 ms total) 80: [ PASSED ] 30 tests. 80: [ SKIPPED ] 1 test, listed below: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80/104 Test #80: MdrunTestsOneRank ......................... Passed 2.05 sec test 81 Start 81: MdrunTestsTwoRanks 81: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 31 tests from 9 test suites. 81: [----------] Global test environment set-up. 81: [----------] 2 tests from AwhTest 81: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 16.1%. 81: The balanceable part of the MD step is 53%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.6%. 81: 81: NOTE: 8.6 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.081 0.020 397.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 88.886 0.270 0.972 0.023 81: [ OK ] AwhTest.SingleBiasMultiDimCanRun (37 ms) 81: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 14.5%. 81: The balanceable part of the MD step is 58%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.4%. 81: 81: NOTE: 8.4 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.058 0.014 397.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 125.228 0.192 0.690 0.032 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 13.8%. 81: The balanceable part of the MD step is 68%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 9.4%. 81: 81: NOTE: 9.4 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 43 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 396.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 200.705 0.120 0.430 0.051 81: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (43 ms) 81: [----------] 2 tests from AwhTest (80 ms total) 81: 81: [----------] 1 test from CompelTest 81: [ RUN ] CompelTest.SwapCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Split0 group 'Ch0' contains 83 atoms. 81: Split1 group 'Ch1' contains 83 atoms. 81: Solvent group 'SOL' contains 11931 atoms. 81: Swap group 'NA+' contains 19 atoms. 81: Swap group 'CL-' contains 19 atoms. 81: Number of degrees of freedom in T-Coupling group System is 27869.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Determining initial numbers of ions per compartment. 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 2 steps, 0.0 ps. 81: Setting the LD random seed to -311115809 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning all bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.4%. 81: The balanceable part of the MD step is 21%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: 81: NOTE: 6 % of the run time was spent in domain decomposition, 81: 26 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.261 0.065 399.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 15.849 1.514 21.806 0.634 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 81: 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Copying channel fluxes from checkpoint file data 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: NOTE: 19 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.170 0.043 399.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 24.385 0.984 14.173 0.975 81: [ OK ] CompelTest.SwapCanRun (407 ms) 81: [----------] 1 test from CompelTest (407 ms total) 81: 81: [----------] 6 tests from BondedInteractionsTest 81: [ RUN ] BondedInteractionsTest.NormalBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 24 % of the run time was spent in domain decomposition, 81: 16 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 379.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 340.590 0.070 0.254 0.016 81: Setting the LD random seed to -277397809 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalBondWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 26 % of the run time was spent in domain decomposition, 81: 16 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 379.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 368.468 0.065 0.234 0.017 81: Setting the LD random seed to -542149639 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedBondWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.NormalAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 24 % of the run time was spent in domain decomposition, 81: 14 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 378.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 373.596 0.064 0.231 0.017 81: Setting the LD random seed to -34136065 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalAngleWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 23 % of the run time was spent in domain decomposition, 81: 14 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 380.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 320.839 0.075 0.269 0.015 81: Setting the LD random seed to 922642350 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 26 % of the run time was spent in domain decomposition, 81: 15 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 380.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 336.792 0.071 0.257 0.016 81: Setting the LD random seed to -1409843319 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalDihedralWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 22 % of the run time was spent in domain decomposition, 81: 12 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 365.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 266.952 0.090 0.324 0.012 81: Setting the LD random seed to 383772583 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (4 ms) 81: [----------] 6 tests from BondedInteractionsTest (26 ms total) 81: 81: [----------] 2 tests from BoxDeformationTest 81: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 30 % of the run time was spent in domain decomposition, 81: 22 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 321.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 910.522 0.026 0.190 0.063 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1141097756 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Setting gen_seed to -1098385025 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (4 ms) 81: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group rest is 1293.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 20 steps, 0.0 ps. 81: Setting the LD random seed to -753143937 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 81: 81: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 81: 81: Estimate for the relative computational load of the PME mesh part: 0.20 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB got disabled because it was unsuitable to use. 81: Average load imbalance: 19.7%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.6%. 81: 81: NOTE: 8.6 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: You can consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.080 0.020 398.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 180.880 0.133 0.955 0.678 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (230 ms) 81: [----------] 2 tests from BoxDeformationTest (234 ms total) 81: 81: [----------] 1 test from PositionRestraintCommTest 81: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any of the VCM groups 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any center of mass motion removal group. 81: This may lead to artifacts. 81: In most cases one should use one group for the whole system. 81: 81: Number of degrees of freedom in T-Coupling group System is 29527.73 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Channel_coco in octane membrane' 81: 10 steps, 0.0 ps. 81: Setting the LD random seed to -1715556498 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 16 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.345 0.086 399.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 22.030 1.089 7.844 1.762 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (354 ms) 81: [----------] 1 test from PositionRestraintCommTest (354 ms total) 81: 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -1687879965 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.045 0.011 398.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 37.855 0.634 2.282 0.010 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -789577859 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 397.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 47.615 0.504 1.815 0.013 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 81: 81: 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (408 ms) 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -335562950 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 43 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.034 0.009 397.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 50.188 0.478 1.722 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -225448017 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 44 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.034 0.008 397.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 50.857 0.472 1.699 0.014 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (42 ms) 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (451 ms total) 81: 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -34340993 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 49 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.049 0.012 398.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 35.129 0.683 2.459 0.002 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -23675157 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 48 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.045 0.011 397.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 38.328 0.626 2.254 0.003 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (34 ms) 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (34 ms total) 81: 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 17.0%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.6%. 81: 81: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.033 0.008 396.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 93.621 0.256 0.923 0.024 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (17 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 17.2%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.5%. 81: 81: NOTE: 7.5 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.009 397.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 89.262 0.269 0.968 0.023 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (18 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 15.1%. 81: The balanceable part of the MD step is 47%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.2%. 81: 81: NOTE: 7.2 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.032 0.008 398.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 98.009 0.245 0.882 0.025 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (16 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 15.3%. 81: The balanceable part of the MD step is 49%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.5%. 81: 81: NOTE: 7.5 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.032 0.008 397.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 97.083 0.247 0.890 0.025 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (16 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 16.2%. 81: The balanceable part of the MD step is 52%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.4%. 81: 81: NOTE: 8.4 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 44 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.032 0.008 398.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 97.428 0.246 0.887 0.025 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (16 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 81: Parrinello-Rahman is not implemented in md-vv. 81: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.033 0.008 396.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 92.464 0.260 0.934 0.024 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (20 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.033 0.008 398.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 93.929 0.256 0.920 0.024 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (19 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.032 0.008 398.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 97.784 0.245 0.884 0.025 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (19 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 398.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 86.073 0.279 1.004 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (37 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 398.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 86.359 0.278 1.000 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (38 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.008 398.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 101.775 0.236 0.849 0.026 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (35 ms) 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest (256 ms total) 81: 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -1140850749 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.3%. 81: The balanceable part of the MD step is 45%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.2%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.034 0.009 397.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 182.026 0.132 0.949 0.006 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (13 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -720913 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.4%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.2%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.008 397.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 198.838 0.121 0.869 0.007 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (12 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to 1341365191 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.4%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.2%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.033 0.008 398.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 185.099 0.130 0.934 0.006 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (12 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -1342439811 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.3%. 81: The balanceable part of the MD step is 52%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.007 397.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 223.199 0.108 0.774 0.008 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (11 ms) 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (50 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 31 tests from 9 test suites ran. (2006 ms total) 81: [ PASSED ] 30 tests. 81: [ SKIPPED ] 1 test, listed below: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81/104 Test #81: MdrunTestsTwoRanks ........................ Passed 2.02 sec test 82 Start 82: MdrunSingleRankAlgorithmsTests 82: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 82: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 600 82: [==========] Running 5 tests from 3 test suites. 82: [----------] Global test environment set-up. 82: [----------] 1 test from DispersionCorrectionTest 82: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 30.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: There are 9 non-linear virtual site constructions. Their contribution to 82: the energy error is approximated. In most cases this does not affect the 82: error significantly. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 82: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 82: 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Alanine dipeptide in vacuo' 82: 200 steps, 0.4 ps. 82: Setting the LD random seed to -272815119 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Converted 3 Bonds with virtual sites to connections, 7 left 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 12 Constraints with virtual sites to connections, 0 left 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 199.3 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 2192.687 0.011 0.079 0.368 82: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (39 ms) 82: [----------] 1 test from DispersionCorrectionTest (39 ms total) 82: 82: [----------] 1 test from OriresTest 82: [ RUN ] OriresTest.OriresCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 518.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There was 1 NOTE 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 82: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 82: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 82: 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 82: 10 steps, 0.0 ps. 82: Setting the LD random seed to -1091078657 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 82: 82: turning H bonds into constraints... 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/orires_1lvz.gro' 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.007 198.6 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 271.082 0.089 0.637 0.337 82: [ OK ] OriresTest.OriresCanRun (298 ms) 82: [----------] 1 test from OriresTest (298 ms total) 82: 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 82: Number of degrees of freedom in T-Coupling group rest is 10.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to -272696588 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: Searching the wall atom type(s) 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.015 199.2 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 293.674 0.082 0.736 0.005 82: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 82: 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (719 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 82: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 82: The supported numbers are > 1. 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 all molecules should be neutral. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 you can only use domain decomposition when there 82: are only small molecules with all bonds constrained (mdrun will check for 82: this). 82: 82: Number of degrees of freedom in T-Coupling group rest is 9.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to 1841201127 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.011 199.0 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 407.963 0.059 0.529 0.008 82: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (254 ms) 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (974 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 5 tests from 3 test suites ran. (1353 ms total) 82: [ PASSED ] 5 tests. 82/104 Test #82: MdrunSingleRankAlgorithmsTests ............ Passed 1.36 sec test 83 Start 83: Minimize1RankTests 83: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/Minimize1RankTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 2 test suites. 83: [----------] Global test environment set-up. 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -4.7991062e+01 83: Maximum force = 1.8629750e+02 on atom 13 83: Norm of force = 8.7721970e+01 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (217 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 3.02330e+02 on atom 3 83: F-Norm = 1.18024e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -5.5862370e+01 83: Maximum force = 4.2727301e+02 on atom 13 83: Norm of force = 1.8452934e+02 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (204 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.1937723e+02 83: Maximum force = 9.9988623e+03 on atom 9 83: Norm of force = 4.6166987e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (51 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: 83: NOTE 2 [file glycine_vacuo.top, line 12]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41575e+04 on atom 10 83: F-Norm = 1.18451e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.5174393e+02 83: Maximum force = 7.4208867e+03 on atom 9 83: Norm of force = 3.5693011e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (49 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.5698462e+02 83: Maximum force = 4.5704999e+02 on atom 17 83: Norm of force = 1.8327331e+02 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (8 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: 83: NOTE 3 [file unknown]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 1.06799e+03 on atom 28 83: F-Norm = 4.26916e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.6941089e+02 83: Maximum force = 2.1831544e+02 on atom 17 83: Norm of force = 7.9209568e+01 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (8 ms) 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (540 ms total) 83: 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents converged to Fmax < 10 in 1 steps 83: Potential Energy = -9.7425687e-01 83: Maximum force = 4.0132279e+00 on atom 1 83: Norm of force = 1.6383933e+00 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (4 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 83: Potential Energy = -9.9064195e-01 83: Maximum force = 2.5781672e+00 on atom 1 83: Norm of force = 1.0525324e+00 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (3 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 83: Potential Energy = -9.9064195e-01 83: Maximum force = 2.5781672e+00 on atom 1 83: Norm of force = 1.0525324e+00 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (3 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.1939685e+02 83: Maximum force = 9.9704248e+03 on atom 9 83: Norm of force = 4.6227543e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (51 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.5625757e+02 83: Maximum force = 7.5018242e+03 on atom 9 83: Norm of force = 3.6139019e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (49 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization has stopped, but the forces have not converged to the 83: requested precision Fmax < 10 (which may not be possible for your system). It 83: stopped because the algorithm tried to make a new step whose size was too 83: small, or there was no change in the energy since last step. Either way, we 83: regard the minimization as converged to within the available machine 83: precision, given your starting configuration and EM parameters. 83: 83: Double precision normally gives you higher accuracy, but this is often not 83: needed for preparing to run molecular dynamics. 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 83: but did not reach the requested Fmax < 10. 83: Potential Energy = 5.6111725e+02 83: Maximum force = 1.2685490e+04 on atom 10 83: Norm of force = 6.0643616e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (49 ms) 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (162 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 2 test suites ran. (728 ms total) 83: [ PASSED ] 12 tests. 83/104 Test #83: Minimize1RankTests ........................ Passed 0.74 sec test 84 Start 84: Minimize2RankTests 84: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/Minimize2RankTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 12 tests from 2 test suites. 84: [----------] Global test environment set-up. 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -4.7990963e+01 84: Maximum force = 1.8629601e+02 on atom 13 84: Norm of force = 8.7721907e+01 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (215 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 3.02331e+02 on atom 3 84: F-Norm = 1.18024e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -5.5862366e+01 84: Maximum force = 4.2726111e+02 on atom 13 84: Norm of force = 1.8452509e+02 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (202 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.1937720e+02 84: Maximum force = 9.9988643e+03 on atom 9 84: Norm of force = 4.6166993e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (52 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: 84: NOTE 2 [file glycine_vacuo.top, line 12]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41575e+04 on atom 10 84: F-Norm = 1.18451e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.5174432e+02 84: Maximum force = 7.4208867e+03 on atom 9 84: Norm of force = 3.5692995e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (49 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.5698450e+02 84: Maximum force = 4.5703549e+02 on atom 17 84: Norm of force = 1.8327631e+02 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (9 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: 84: NOTE 3 [file unknown]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 1.06799e+03 on atom 28 84: F-Norm = 4.26916e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.6941107e+02 84: Maximum force = 2.1831662e+02 on atom 17 84: Norm of force = 7.9213110e+01 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (10 ms) 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (539 ms total) 84: 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents converged to Fmax < 10 in 1 steps 84: Potential Energy = -9.7425687e-01 84: Maximum force = 4.0132279e+00 on atom 3 84: Norm of force = 1.6383933e+00 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (4 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 4.01323e+00 on atom 3 84: F-Norm = 1.63839e+00 84: 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 84: Potential Energy = -9.9064195e-01 84: Maximum force = 2.5781672e+00 on atom 3 84: Norm of force = 1.0525324e+00 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (4 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.1939673e+02 84: Maximum force = 9.9704229e+03 on atom 9 84: Norm of force = 4.6227558e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (51 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41672e+04 on atom 10 84: F-Norm = 1.19357e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.5625764e+02 84: Maximum force = 7.5018237e+03 on atom 9 84: Norm of force = 3.6139019e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (50 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (46 ms) 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (159 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 12 tests from 2 test suites ran. (725 ms total) 84: [ PASSED ] 12 tests. 84/104 Test #84: Minimize2RankTests ........................ Passed 0.74 sec test 85 Start 85: MdrunNonIntegratorTests 85: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 46 tests from 3 test suites. 85: [----------] Global test environment set-up. 85: [----------] 1 test from NonbondedBenchTest 85: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 85: SIMD width: 4 85: System size: 3000 atoms 85: Cut-off radius: 1 nm 85: Number of threads: 1 85: Number of iterations: 1 85: Compute energies: no 85: Ewald excl. corr.: analytical 85: 85: Coulomb LJ comb. SIMD intmod. Mcycles Mcycles/it. pairs/cycle 85: total useful 85: Ewald all geom. 4xM PotShift 9.085 9.0852 0.1310 0.0693 85: [ OK ] NonbondedBenchTest.BasicEndToEndTest (14 ms) 85: [----------] 1 test from NonbondedBenchTest (14 ms total) 85: 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.370 0.179 0.643 0.019 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 85: 85: trr version: GMX_trn_file (single precision) 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 30 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4940.332 0.005 0.017 0.686 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (17 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.008 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 175.611 0.137 0.492 0.024 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 27 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4771.955 0.005 0.018 0.663 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (13 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.008 199.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 175.891 0.136 0.491 0.024 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 27 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 193.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4503.358 0.005 0.019 0.625 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (14 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 193.383 0.124 0.447 0.027 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 31 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4213.812 0.006 0.021 0.585 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (13 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 166.791 0.144 0.518 0.029 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 28 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4013.416 0.006 0.022 0.697 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (225 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 199.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 164.274 0.146 0.526 0.029 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 41 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3569.290 0.007 0.024 0.620 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (211 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.009 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 172.223 0.139 0.502 0.030 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 26 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 193.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4338.446 0.006 0.020 0.753 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (219 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.008 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 175.977 0.136 0.491 0.031 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 29 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3911.488 0.006 0.022 0.679 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (220 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.136 0.179 0.644 0.045 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 194.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2338.874 0.010 0.037 0.785 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (23 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.009 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 156.850 0.153 0.551 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 194.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2437.908 0.010 0.035 0.818 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (20 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 152.952 0.157 0.565 0.051 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 24 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 192.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2926.648 0.008 0.030 0.982 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (77 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 126.821 0.189 0.681 0.043 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 24 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 193.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2668.079 0.009 0.032 0.896 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (44 ms) 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1102 ms total) 85: 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 138.771 0.173 0.623 0.058 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2342.431 0.010 0.037 0.976 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 122.108 0.197 0.708 0.051 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2351.372 0.010 0.037 0.980 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 145.923 0.164 0.592 0.061 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2144.307 0.011 0.040 0.893 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 135.831 0.177 0.636 0.057 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2432.133 0.010 0.036 1.013 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.010 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 141.139 0.170 0.612 0.059 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2342.431 0.010 0.037 0.976 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 144.819 0.166 0.597 0.060 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 23 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2355.868 0.010 0.037 0.982 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 137.879 0.174 0.627 0.057 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2151.797 0.011 0.040 0.897 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 127.322 0.188 0.679 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 23 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2186.934 0.011 0.040 0.911 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 198.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 143.865 0.167 0.601 0.060 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 177.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2062.469 0.012 0.042 0.859 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.010 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 142.320 0.169 0.607 0.059 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2244.296 0.011 0.038 0.935 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 131.758 0.182 0.656 0.055 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2173.049 0.011 0.040 0.905 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 132.529 0.181 0.652 0.055 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 183.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2177.658 0.011 0.040 0.907 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 116.565 0.206 0.741 0.049 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2259.939 0.011 0.038 0.942 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.177 0.179 0.644 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2664.617 0.009 0.032 1.110 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 126.226 0.190 0.684 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2262.429 0.011 0.038 0.943 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 133.398 0.180 0.648 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2294.448 0.010 0.038 0.956 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 129.699 0.185 0.666 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2280.857 0.011 0.038 0.950 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 137.679 0.174 0.628 0.057 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2274.121 0.011 0.038 0.948 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 138.815 0.173 0.622 0.058 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2267.425 0.011 0.038 0.945 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 132.688 0.181 0.651 0.055 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2677.355 0.009 0.032 1.116 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 128.675 0.187 0.671 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2153.301 0.011 0.040 0.897 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 128.092 0.187 0.675 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 181.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2065.927 0.012 0.042 0.861 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 138.824 0.173 0.622 0.058 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1889.173 0.013 0.046 0.787 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (30 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 128.282 0.187 0.674 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2324.752 0.010 0.037 0.969 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (30 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 114.684 0.209 0.753 0.048 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 182.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2428.299 0.010 0.036 1.012 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.731 0.178 0.641 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2048.751 0.012 0.042 0.854 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (30 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.010 198.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 141.227 0.170 0.612 0.059 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2017.882 0.012 0.043 0.841 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (29 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 198.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 132.241 0.181 0.653 0.055 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2212.062 0.011 0.039 0.922 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (31 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 117.392 0.204 0.736 0.049 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 183.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2372.196 0.010 0.036 0.988 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 127.036 0.189 0.680 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 183.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2196.290 0.011 0.039 0.915 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (31 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 133.274 0.180 0.648 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 183.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2128.747 0.011 0.041 0.887 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (31 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 119.479 0.201 0.723 0.050 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 184.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2224.041 0.011 0.039 0.927 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.640 0.178 0.642 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 182.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2182.286 0.011 0.040 0.909 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (31 ms) 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (838 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 46 tests from 3 test suites ran. (1982 ms total) 85: [ PASSED ] 46 tests. 85/104 Test #85: MdrunNonIntegratorTests ................... Passed 2.00 sec test 86 Start 86: MdrunTpiTests 86: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunTpiTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 3 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 3 tests from Simple/TpiTest 86: [ RUN ] Simple/TpiTest.ReproducesOutput/0 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/0 (228 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/1 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/1 (211 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/2 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/2 (214 ms) 86: [----------] 3 tests from Simple/TpiTest (654 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 3 tests from 1 test suite ran. (667 ms total) 86: [ PASSED ] 3 tests. 86/104 Test #86: MdrunTpiTests ............................. Passed 0.68 sec test 87 Start 87: MdrunMpiTests 87: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunMpiTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 16 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from MimicTest 87: [ RUN ] MimicTest.OneQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 22 % of the run time was spent in domain decomposition, 87: 14 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 379.5 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 308.809 0.078 0.280 0.043 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -9439235 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.OneQuantumMol (5 ms) 87: [ RUN ] MimicTest.AllQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 26 % of the run time was spent in domain decomposition, 87: 14 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 359.2 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 364.026 0.066 0.237 0.051 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -675546305 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.AllQuantumMol (4 ms) 87: [ RUN ] MimicTest.TwoQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 26 % of the run time was spent in domain decomposition, 87: 18 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 382.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 347.281 0.069 0.249 0.048 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -540229633 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.TwoQuantumMol (4 ms) 87: [ RUN ] MimicTest.BondCuts 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 66.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: NVE simulation: will use the initial temperature of 300.368 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 87: 87: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 22 % of the run time was spent in domain decomposition, 87: 14 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 384.1 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 300.114 0.080 0.288 0.080 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -68214785 87: 87: Generated 2211 of the 2211 non-bonded parameter combinations 87: 87: Generated 2211 of the 2211 1-4 parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.BondCuts (10 ms) 87: [----------] 4 tests from MimicTest (25 ms total) 87: 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: There was 1 NOTE 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There were 2 NOTEs 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There was 1 NOTE 87: Setting the LD random seed to 669753303 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -597754154 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -339743239 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -721437185 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.5%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.3%. 87: 87: 87: NOTE: 45 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.035 0.009 398.8 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 205.719 0.117 0.420 0.014 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (11 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 43 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.022 0.006 398.1 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 327.748 0.073 0.264 0.023 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (8 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 10%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.1%. 87: 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.044 0.011 396.4 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 164.231 0.146 0.526 0.011 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (171 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.043 0.011 397.5 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 167.743 0.143 0.515 0.012 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (116 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.046 0.012 398.7 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 156.547 0.153 0.552 0.011 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (27 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.041 0.010 397.6 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 173.875 0.138 0.497 0.012 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (22 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (357 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 16 tests from 2 test suites ran. (418 ms total) 87: [ PASSED ] 10 tests. 87: [ SKIPPED ] 6 tests, listed below: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87/104 Test #87: MdrunMpiTests ............................. Passed 0.43 sec test 88 Start 88: MdrunMultiSimTests 88: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 2 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from InNvt/MultiSimTerminationTest 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 88: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 2 tests from 1 test suite ran. (14 ms total) 88: [ PASSED ] 2 tests. 88: 88: YOU HAVE 4 DISABLED TESTS 88: 88/104 Test #88: MdrunMultiSimTests ........................ Passed 0.02 sec test 89 Start 89: MdrunMultiSimReplexTests 89: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 1 test from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 89: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 89: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 1 test from 1 test suite ran. (13 ms total) 89: [ PASSED ] 1 test. 89: 89: YOU HAVE 4 DISABLED TESTS 89: 89/104 Test #89: MdrunMultiSimReplexTests .................. Passed 0.02 sec test 90 Start 90: MdrunMultiSimReplexEquivalenceTests 90: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 0 tests from 0 test suites. 90: [==========] 0 tests from 0 test suites ran. (0 ms total) 90: [ PASSED ] 0 tests. 90: 90: YOU HAVE 10 DISABLED TESTS 90: 90/104 Test #90: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.01 sec test 91 Start 91: MdrunMpi1RankPmeTests 91: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 91: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 19 tests from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 19 tests from ReproducesEnergies/PmeTest 91: Number of degrees of freedom in T-Coupling group rest is 12.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 1046.791 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 2 NOTEs 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: For a correct single-point energy evaluation with nsteps = 0, use 91: continuation = yes to avoid constraining the input coordinates. 91: 91: Number of degrees of freedom in T-Coupling group rest is 13.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 966.268 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 3 NOTEs 91: Setting the LD random seed to -541143701 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: Setting the LD random seed to -407160834 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: Searching the wall atom type(s) 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.029 0.015 199.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 124.025 0.194 0.697 0.009 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (175 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.025 0.013 199.0 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 144.123 0.167 0.599 0.010 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (17 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.003 0.001 192.5 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 61.370 0.391 1.408 0.004 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (579 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.029 0.014 199.5 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 126.829 0.189 0.681 0.009 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (18 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [----------] 19 tests from ReproducesEnergies/PmeTest (792 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 19 tests from 1 test suite ran. (812 ms total) 91: [ PASSED ] 4 tests. 91: [ SKIPPED ] 15 tests, listed below: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91/104 Test #91: MdrunMpi1RankPmeTests ..................... Passed 0.82 sec test 92 Start 92: MdrunMpi2RankPmeTests 92: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 19 tests from 1 test suite. 92: [----------] Global test environment set-up. 92: [----------] 19 tests from ReproducesEnergies/PmeTest 92: Number of degrees of freedom in T-Coupling group rest is 12.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 1046.791 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 2 NOTEs 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: For a correct single-point energy evaluation with nsteps = 0, use 92: continuation = yes to avoid constraining the input coordinates. 92: 92: Number of degrees of freedom in T-Coupling group rest is 13.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 966.268 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 3 NOTEs 92: Setting the LD random seed to -72000017 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: Setting the LD random seed to -437026881 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: Searching the wall atom type(s) 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 9.6%. 92: The balanceable part of the MD step is 13%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.2%. 92: 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.047 0.012 398.3 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 155.141 0.155 0.557 0.011 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (175 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.3%. 92: The balanceable part of the MD step is 12%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.0%. 92: 92: 92: NOTE: 26 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.042 0.011 397.8 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 170.086 0.141 0.508 0.012 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (17 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.004 0.001 371.6 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 73.143 0.328 1.181 0.005 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (562 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.053 0.013 398.0 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 135.513 0.177 0.638 0.009 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (125 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.047 0.012 397.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 155.184 0.155 0.557 0.011 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (16 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.005 0.001 378.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 65.448 0.367 1.320 0.005 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (350 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 10.3%. 92: The balanceable part of the MD step is 12%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.2%. 92: 92: 92: NOTE: 26 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.044 0.011 398.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 165.815 0.145 0.521 0.012 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (17 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [----------] 19 tests from ReproducesEnergies/PmeTest (1268 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 19 tests from 1 test suite ran. (1287 ms total) 92: [ PASSED ] 7 tests. 92: [ SKIPPED ] 12 tests, listed below: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92/104 Test #92: MdrunMpi2RankPmeTests ..................... Passed 1.30 sec test 93 Start 93: MdrunMpi4RankPmeTests 93: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "1" "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunMpi4RankPmeTests.xml" 93: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 93: Test timeout computed to be: 600 93: [==========] Running 19 tests from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 19 tests from ReproducesEnergies/PmeTest 93: Number of degrees of freedom in T-Coupling group rest is 12.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 1046.791 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 2 NOTEs 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: For a correct single-point energy evaluation with nsteps = 0, use 93: continuation = yes to avoid constraining the input coordinates. 93: 93: Number of degrees of freedom in T-Coupling group rest is 13.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 966.268 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 3 NOTEs 93: Setting the LD random seed to -352555009 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: Setting the LD random seed to 1331420402 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: Searching the wall atom type(s) 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 7.4%. 93: The balanceable part of the MD step is 9%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.7%. 93: 93: 93: NOTE: 51 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.051 0.013 398.5 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 142.228 0.169 0.607 0.010 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (171 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 14.1%. 93: The balanceable part of the MD step is 9%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 1.3%. 93: 93: 93: NOTE: 47 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.046 0.012 397.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 155.902 0.154 0.554 0.011 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (18 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.004 0.001 350.1 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 82.912 0.289 1.042 0.006 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (571 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 20.7%. 93: The balanceable part of the MD step is 3%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.7%. 93: Average PME mesh/force load: 49.090 93: Part of the total run time spent waiting due to PP/PME imbalance: 70.5 % 93: 93: NOTE: 70.5 % performance was lost because the PME ranks 93: had more work to do than the PP ranks. 93: You might want to increase the number of PME ranks 93: or increase the cut-off and the grid spacing. 93: 93: 93: NOTE: 22 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.071 0.018 399.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 101.706 0.236 0.850 0.007 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (72 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 23.0%. 93: The balanceable part of the MD step is 4%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.9%. 93: Average PME mesh/force load: 48.385 93: Part of the total run time spent waiting due to PP/PME imbalance: 70.2 % 93: 93: NOTE: 70.2 % performance was lost because the PME ranks 93: had more work to do than the PP ranks. 93: You might want to increase the number of PME ranks 93: or increase the cut-off and the grid spacing. 93: 93: 93: NOTE: 20 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.065 0.016 398.3 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 110.971 0.216 0.779 0.008 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (20 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.008 0.002 385.7 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 42.654 0.563 2.026 0.003 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (110 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 8.5%. 93: The balanceable part of the MD step is 7%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.6%. 93: 93: 93: NOTE: 39 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.047 0.012 398.4 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 155.240 0.155 0.557 0.011 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (19 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [----------] 19 tests from ReproducesEnergies/PmeTest (985 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 19 tests from 1 test suite ran. (1005 ms total) 93: [ PASSED ] 7 tests. 93: [ SKIPPED ] 12 tests, listed below: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93/104 Test #93: MdrunMpi4RankPmeTests ..................... Passed 1.02 sec test 94 Start 94: MdrunCoordinationBasicTests1Rank 94: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 94: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 94: Test timeout computed to be: 1920 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest 94: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.010 0.010 99.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 140.080 0.171 0.617 0.019 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.006 0.006 99.5 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 236.437 0.102 0.365 0.033 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 4. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 4. 94: 94: 94: There were 4 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.005 0.005 98.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 267.317 0.090 0.323 0.037 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.008 0.008 99.5 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 180.277 0.133 0.479 0.025 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.007 0.007 99.5 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 207.260 0.116 0.417 0.029 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.008 0.008 99.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 188.848 0.127 0.458 0.026 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (69 ms) 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest (69 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (83 ms total) 94: [ PASSED ] 1 test. 94/104 Test #94: MdrunCoordinationBasicTests1Rank .......... Passed 0.10 sec test 95 Start 95: MdrunCoordinationBasicTests2Ranks 95: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 95: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 95: Test timeout computed to be: 1920 95: [==========] Running 1 test from 1 test suite. 95: [----------] Global test environment set-up. 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest 95: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.4%. 95: The balanceable part of the MD step is 54%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.8%. 95: 95: 95: NOTE: 46 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.009 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 160.176 0.150 0.539 0.022 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 3.0%. 95: The balanceable part of the MD step is 52%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 1.6%. 95: 95: 95: NOTE: 45 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.006 198.9 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 248.802 0.096 0.347 0.035 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 4 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was turned on during the run due to measured imbalance. 95: Average load imbalance: 4.6%. 95: The balanceable part of the MD step is 49%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 2.2%. 95: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 95: 95: 95: NOTE: 45 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.006 199.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 258.192 0.093 0.335 0.036 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 0.9%. 95: The balanceable part of the MD step is 48%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.4%. 95: 95: 95: NOTE: 47 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.008 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 178.188 0.135 0.485 0.025 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 3.9%. 95: The balanceable part of the MD step is 50%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 2.0%. 95: 95: 95: NOTE: 46 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.008 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 187.013 0.128 0.462 0.026 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.1%. 95: The balanceable part of the MD step is 49%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.5%. 95: 95: 95: NOTE: 47 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.008 198.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 194.999 0.123 0.443 0.027 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (71 ms) 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest (71 ms total) 95: 95: [----------] Global test environment tear-down 95: [==========] 1 test from 1 test suite ran. (86 ms total) 95: [ PASSED ] 1 test. 95/104 Test #95: MdrunCoordinationBasicTests2Ranks ......... Passed 0.10 sec test 96 Start 96: MdrunCoordinationCouplingTests1Rank 96: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 96: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 96: Test timeout computed to be: 1920 96: [==========] Running 25 tests from 1 test suite. 96: [----------] Global test environment set-up. 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 162.446 0.148 0.532 0.023 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 267.503 0.090 0.323 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 297.771 0.081 0.290 0.041 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 200.377 0.120 0.431 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 177.370 0.135 0.487 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 216.366 0.111 0.399 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.736 0.126 0.453 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 234.350 0.102 0.369 0.033 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 254.770 0.094 0.339 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.392 0.127 0.459 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 205.696 0.117 0.420 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 185.370 0.129 0.466 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.814 0.117 0.422 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 260.512 0.092 0.332 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 273.064 0.088 0.316 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 218.973 0.110 0.395 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.865 0.127 0.457 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 194.126 0.124 0.445 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (62 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 147.365 0.163 0.586 0.020 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 267.306 0.090 0.323 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 264.710 0.091 0.326 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.170 0.112 0.403 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 184.239 0.130 0.469 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 120.052 0.200 0.720 0.017 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (69 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.809 0.128 0.463 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 206.884 0.116 0.418 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 293.837 0.082 0.294 0.041 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 183.789 0.131 0.470 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.817 0.125 0.450 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 200.534 0.120 0.431 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 178.346 0.135 0.484 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 264.687 0.091 0.326 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 278.344 0.086 0.310 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 199.585 0.120 0.433 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 217.958 0.110 0.396 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.632 0.125 0.451 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.171 0.129 0.464 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 263.521 0.091 0.328 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 236.873 0.101 0.365 0.033 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.487 0.129 0.463 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 183.356 0.131 0.471 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 222.597 0.108 0.388 0.031 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (68 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 203.562 0.118 0.424 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 296.810 0.081 0.291 0.041 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 275.469 0.087 0.314 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 207.798 0.115 0.416 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.447 0.117 0.423 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 197.759 0.121 0.437 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 187.531 0.128 0.461 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 199.140 0.121 0.434 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 302.257 0.079 0.286 0.042 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 217.766 0.110 0.397 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 192.404 0.125 0.449 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 203.226 0.118 0.425 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (68 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 212.603 0.113 0.406 0.030 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 270.427 0.089 0.319 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 283.768 0.085 0.304 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.194 0.129 0.464 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.630 0.123 0.442 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 216.922 0.111 0.398 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (62 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.977 0.117 0.422 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 257.507 0.093 0.336 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 284.095 0.084 0.304 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 160.486 0.150 0.538 0.022 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.165 0.126 0.454 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.042 0.129 0.464 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 175.456 0.137 0.492 0.024 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 274.904 0.087 0.314 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 269.221 0.089 0.321 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 194.968 0.123 0.443 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 180.869 0.133 0.478 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 201.169 0.119 0.429 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 180.843 0.133 0.478 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 279.595 0.086 0.309 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 269.669 0.089 0.320 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 200.110 0.120 0.432 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 198.934 0.121 0.434 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.997 0.133 0.480 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 162.146 0.148 0.533 0.023 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 255.330 0.094 0.338 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 273.246 0.088 0.316 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 159.069 0.151 0.543 0.022 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 209.309 0.115 0.413 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 210.611 0.114 0.410 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.650 0.125 0.451 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 258.111 0.093 0.335 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 276.707 0.087 0.312 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.821 0.124 0.446 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.894 0.127 0.457 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 184.626 0.130 0.468 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (63 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.894 0.124 0.446 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 247.026 0.097 0.350 0.034 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 277.629 0.086 0.311 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 155.799 0.154 0.555 0.022 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.391 0.129 0.464 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.738 0.127 0.458 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (69 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.408 0.129 0.463 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 251.391 0.095 0.344 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 297.484 0.081 0.290 0.041 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 176.017 0.136 0.491 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 203.966 0.118 0.424 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.269 0.134 0.482 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (66 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 199.159 0.121 0.434 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 261.730 0.092 0.330 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 283.572 0.085 0.305 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 185.231 0.130 0.466 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 172.963 0.139 0.500 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 171.523 0.140 0.504 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (68 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.471 0.126 0.454 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 258.273 0.093 0.335 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 260.611 0.092 0.332 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 185.493 0.129 0.466 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 197.196 0.122 0.438 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.644 0.125 0.451 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 180.753 0.133 0.478 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 236.038 0.102 0.366 0.033 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 243.194 0.099 0.355 0.034 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 196.510 0.122 0.440 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.861 0.133 0.480 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.207 0.124 0.447 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (66 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 162.772 0.147 0.531 0.023 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 233.197 0.103 0.371 0.032 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 249.649 0.096 0.346 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.412 0.126 0.454 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 173.548 0.138 0.498 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.610 0.112 0.403 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (67 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 157.110 0.153 0.550 0.022 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 223.891 0.107 0.386 0.031 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 232.950 0.103 0.371 0.032 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.878 0.126 0.453 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.054 0.126 0.455 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 184.289 0.130 0.469 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (73 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.672 0.134 0.481 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 263.905 0.091 0.327 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 275.100 0.087 0.314 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 187.949 0.128 0.460 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.035 0.134 0.483 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 185.309 0.130 0.466 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 165.225 0.145 0.523 0.023 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 229.359 0.105 0.377 0.032 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 220.289 0.109 0.392 0.031 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 164.502 0.146 0.525 0.023 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.010 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 154.204 0.156 0.560 0.021 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 174.640 0.137 0.495 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (71 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.196 0.123 0.443 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 262.399 0.091 0.329 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 257.013 0.093 0.336 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 187.332 0.128 0.461 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 185.225 0.130 0.466 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 164.072 0.146 0.527 0.023 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (67 ms) 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (1658 ms total) 96: 96: [----------] Global test environment tear-down 96: [==========] 25 tests from 1 test suite ran. (1673 ms total) 96: [ PASSED ] 25 tests. 96/104 Test #96: MdrunCoordinationCouplingTests1Rank ....... Passed 1.68 sec test 97 Start 97: MdrunCoordinationCouplingTests2Ranks 97: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 97: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 97: Test timeout computed to be: 1920 97: [==========] Running 25 tests from 1 test suite. 97: [----------] Global test environment set-up. 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 8.1%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 4.0%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.012 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 127.389 0.188 0.678 0.018 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 262.186 0.092 0.330 0.036 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.2%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.5%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 249.114 0.096 0.347 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 205.264 0.117 0.421 0.029 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 41%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 199.601 0.120 0.433 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 4.0%. 97: The balanceable part of the MD step is 42%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.7%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 199.653 0.120 0.433 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (69 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.9%. 97: The balanceable part of the MD step is 55%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.5%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 183.638 0.131 0.470 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 284.495 0.084 0.304 0.040 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.6%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 275.889 0.087 0.313 0.038 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.9%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.4%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.121 0.126 0.454 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.8%. 97: The balanceable part of the MD step is 47%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.3%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 196.896 0.122 0.439 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 4.2%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 2.0%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 172.201 0.139 0.502 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (67 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 56%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 172.541 0.139 0.501 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 193.699 0.124 0.446 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.2%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 241.620 0.099 0.358 0.034 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 47%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 212.153 0.113 0.407 0.029 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.3%. 97: The balanceable part of the MD step is 47%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.612 0.126 0.453 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 6.5%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 3.2%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 175.059 0.137 0.494 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (69 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.0%. 97: The balanceable part of the MD step is 56%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 189.167 0.127 0.457 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.8%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.4%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 282.124 0.085 0.306 0.039 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 3.2%. 97: The balanceable part of the MD step is 43%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.4%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 271.685 0.088 0.318 0.038 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.7%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.3%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 207.788 0.116 0.416 0.029 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 176.077 0.136 0.491 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.8%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.4%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 201.412 0.119 0.429 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (65 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.912 0.128 0.460 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 280.486 0.086 0.308 0.039 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 224.556 0.107 0.385 0.031 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 179.884 0.133 0.480 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 189.881 0.126 0.455 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 182.896 0.131 0.472 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (70 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 171.268 0.140 0.504 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 274.646 0.087 0.315 0.038 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 276.806 0.087 0.312 0.038 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.168 0.126 0.454 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 192.365 0.125 0.449 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 188.469 0.127 0.458 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (67 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 186.380 0.129 0.464 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 240.137 0.100 0.360 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 250.502 0.096 0.345 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 192.434 0.125 0.449 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 200.452 0.120 0.431 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 183.967 0.130 0.470 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (67 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 170.304 0.141 0.507 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 240.634 0.100 0.359 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 253.658 0.095 0.341 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 178.874 0.134 0.483 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 177.436 0.135 0.487 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 203.804 0.118 0.424 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (70 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 189.928 0.126 0.455 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 233.374 0.103 0.370 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 277.592 0.086 0.311 0.039 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 181.282 0.132 0.477 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 181.565 0.132 0.476 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 166.841 0.144 0.518 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (71 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 181.846 0.132 0.475 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 248.978 0.096 0.347 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 289.006 0.083 0.299 0.040 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 199.072 0.121 0.434 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 191.778 0.125 0.451 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 198.268 0.121 0.436 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (66 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 172.508 0.139 0.501 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 245.898 0.098 0.351 0.034 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 257.131 0.093 0.336 0.036 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 198.703 0.121 0.435 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 193.389 0.124 0.447 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.521 0.130 0.468 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (68 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 185.862 0.129 0.465 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 266.941 0.090 0.324 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 256.200 0.094 0.337 0.036 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.014 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 102.315 0.235 0.844 0.014 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 176.866 0.136 0.489 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.625 0.133 0.478 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (78 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 177.805 0.135 0.486 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 274.365 0.087 0.315 0.038 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 231.728 0.104 0.373 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.707 0.126 0.453 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 167.560 0.143 0.516 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 182.802 0.131 0.473 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (70 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 170.194 0.141 0.508 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 240.132 0.100 0.360 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 204.555 0.117 0.422 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 170.229 0.141 0.508 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 156.519 0.153 0.552 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 156.647 0.153 0.552 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (79 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 164.671 0.146 0.525 0.023 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 204.793 0.117 0.422 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 226.015 0.106 0.382 0.031 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 176.554 0.136 0.489 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 158.748 0.151 0.544 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 159.291 0.151 0.542 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (78 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 152.205 0.158 0.568 0.021 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 263.144 0.091 0.328 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 240.493 0.100 0.359 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 185.022 0.130 0.467 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 209.505 0.115 0.412 0.029 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.703 0.142 0.512 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (77 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.7%. 97: The balanceable part of the MD step is 62%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.4%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 179.536 0.134 0.481 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 59%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 218.360 0.110 0.396 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 54%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 214.162 0.112 0.403 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 171.401 0.140 0.504 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.2%. 97: The balanceable part of the MD step is 54%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 155.514 0.154 0.556 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.499 0.142 0.513 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (74 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 60%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 156.354 0.153 0.553 0.022 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.8%. 97: The balanceable part of the MD step is 58%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.6%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 220.289 0.109 0.392 0.031 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 3.1%. 97: The balanceable part of the MD step is 59%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.9%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 215.794 0.111 0.400 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 56%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.3%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 170.613 0.141 0.506 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 3.5%. 97: The balanceable part of the MD step is 56%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 2.0%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 181.162 0.132 0.477 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.8%. 97: The balanceable part of the MD step is 60%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.5%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.021 0.139 0.499 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (75 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.9%. 97: The balanceable part of the MD step is 60%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.5%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 197.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 159.874 0.150 0.540 0.022 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.3%. 97: The balanceable part of the MD step is 61%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.2%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 238.132 0.101 0.363 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.0%. 97: The balanceable part of the MD step is 60%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 221.632 0.108 0.390 0.031 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.0%. 97: The balanceable part of the MD step is 57%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 167.208 0.144 0.517 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.0%. 97: The balanceable part of the MD step is 58%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.514 0.152 0.549 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.5%. 97: The balanceable part of the MD step is 58%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.3%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 171.073 0.140 0.505 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (74 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 153.719 0.156 0.562 0.021 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 214.278 0.112 0.403 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 266.416 0.090 0.324 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 177.248 0.135 0.487 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.892 0.130 0.467 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 166.521 0.144 0.519 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (73 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.332 0.133 0.479 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 282.667 0.085 0.306 0.039 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 255.176 0.094 0.339 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 185.117 0.130 0.467 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 133.659 0.180 0.646 0.019 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 176.932 0.136 0.488 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (71 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.511 0.138 0.498 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 249.275 0.096 0.347 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 196.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 250.187 0.096 0.345 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.012 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 127.032 0.189 0.680 0.018 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.170 0.130 0.469 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 181.975 0.132 0.475 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (73 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.011 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 138.793 0.173 0.623 0.019 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 217.962 0.110 0.396 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 232.317 0.103 0.372 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.313 0.153 0.549 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 154.295 0.156 0.560 0.021 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 179.369 0.134 0.482 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (75 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 163.719 0.147 0.528 0.023 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 228.683 0.105 0.378 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 221.445 0.108 0.390 0.031 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 159.966 0.150 0.540 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 169.534 0.142 0.510 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 158.053 0.152 0.547 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (73 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.733 0.142 0.512 0.023 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 195.128 0.123 0.443 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 217.240 0.110 0.398 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 174.220 0.138 0.496 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 159.682 0.150 0.541 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 154.055 0.156 0.561 0.021 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (78 ms) 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (1807 ms total) 97: 97: [----------] Global test environment tear-down 97: [==========] 25 tests from 1 test suite ran. (1821 ms total) 97: [ PASSED ] 25 tests. 97/104 Test #97: MdrunCoordinationCouplingTests2Ranks ...... Passed 1.83 sec test 98 Start 98: MdrunCoordinationConstraintsTests1Rank 98: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 98: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 98: Test timeout computed to be: 1920 98: [==========] Running 13 tests from 1 test suite. 98: [----------] Global test environment set-up. 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 167.457 0.143 0.516 0.029 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 211.537 0.113 0.408 0.037 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 249.913 0.096 0.346 0.043 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 184.892 0.130 0.467 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 186.076 0.129 0.464 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 175.485 0.137 0.492 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1264 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 181.386 0.132 0.476 0.031 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 236.047 0.102 0.366 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 232.748 0.103 0.371 0.040 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 194.968 0.123 0.443 0.034 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 185.694 0.129 0.465 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 170.867 0.140 0.506 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1333 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 135.463 0.177 0.638 0.024 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 200.013 0.120 0.432 0.035 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 261.197 0.092 0.331 0.045 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 165.768 0.145 0.521 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 161.036 0.149 0.537 0.028 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 174.848 0.137 0.494 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1306 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 145.493 0.165 0.594 0.025 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 223.169 0.108 0.387 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 222.951 0.108 0.388 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 176.658 0.136 0.489 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 173.645 0.138 0.498 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 178.744 0.134 0.483 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1275 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 185.086 0.130 0.467 0.032 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 245.198 0.098 0.352 0.043 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 235.012 0.102 0.368 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 189.411 0.127 0.456 0.033 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 140.170 0.171 0.616 0.024 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 169.340 0.142 0.510 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1274 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 158.852 0.151 0.544 0.028 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 251.063 0.096 0.344 0.044 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 238.552 0.101 0.362 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 191.889 0.125 0.450 0.033 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 184.587 0.130 0.468 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 98.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 184.548 0.130 0.468 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1276 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 186.583 0.129 0.463 0.032 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 221.341 0.108 0.390 0.038 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 236.891 0.101 0.365 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 183.493 0.131 0.471 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 181.205 0.132 0.477 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 192.543 0.125 0.449 0.033 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1248 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 123.380 0.195 0.700 0.021 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 175.470 0.137 0.492 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 237.751 0.101 0.363 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 158.876 0.151 0.544 0.028 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.009 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 172.204 0.139 0.502 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 209.117 0.115 0.413 0.036 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1337 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 167.695 0.143 0.515 0.029 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 246.414 0.097 0.351 0.043 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 146.754 0.164 0.589 0.025 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 140.454 0.171 0.615 0.024 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 161.763 0.148 0.534 0.028 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 126.719 0.189 0.682 0.022 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1265 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 179.150 0.134 0.482 0.031 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 150.545 0.159 0.574 0.026 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 238.773 0.101 0.362 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 163.277 0.147 0.529 0.028 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 169.643 0.141 0.509 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 171.983 0.140 0.502 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1301 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 153.260 0.157 0.564 0.027 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 212.889 0.113 0.406 0.037 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 219.543 0.109 0.394 0.038 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 160.369 0.150 0.539 0.028 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 141.412 0.170 0.611 0.025 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 167.376 0.143 0.516 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1323 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 158.611 0.151 0.545 0.028 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 231.985 0.103 0.372 0.040 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 222.180 0.108 0.389 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 171.911 0.140 0.503 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 153.497 0.156 0.563 0.027 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 167.886 0.143 0.515 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1285 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 167.162 0.144 0.517 0.029 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 230.967 0.104 0.374 0.040 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.007 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 225.160 0.107 0.384 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 168.969 0.142 0.511 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 167.257 0.143 0.517 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 157.138 0.153 0.550 0.027 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1242 ms) 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (16736 ms total) 98: 98: [----------] Global test environment tear-down 98: [==========] 13 tests from 1 test suite ran. (16750 ms total) 98: [ PASSED ] 13 tests. 98/104 Test #98: MdrunCoordinationConstraintsTests1Rank .... Passed 16.76 sec test 99 Start 99: MdrunCoordinationConstraintsTests2Ranks 99: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 99: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 99: Test timeout computed to be: 1920 99: [==========] Running 13 tests from 1 test suite. 99: [----------] Global test environment set-up. 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.1%. 99: The balanceable part of the MD step is 53%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 158.106 0.152 0.546 0.027 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.6%. 99: The balanceable part of the MD step is 43%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.2%. 99: 99: 99: NOTE: 44 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 252.794 0.095 0.342 0.044 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB got disabled because it was unsuitable to use. 99: Average load imbalance: 5.2%. 99: The balanceable part of the MD step is 42%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 2.2%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 240.794 0.100 0.359 0.042 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 42%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 158.721 0.151 0.544 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.1%. 99: The balanceable part of the MD step is 44%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 158.580 0.151 0.545 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.1%. 99: The balanceable part of the MD step is 41%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 172.670 0.139 0.500 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1302 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.3%. 99: The balanceable part of the MD step is 55%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.1%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 158.234 0.152 0.546 0.027 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.9%. 99: The balanceable part of the MD step is 49%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 45 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 235.754 0.102 0.366 0.041 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.5%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.2%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 204.216 0.118 0.423 0.035 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.9%. 99: The balanceable part of the MD step is 47%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.4%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 179.369 0.134 0.482 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.9%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.3%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 169.170 0.142 0.511 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.7%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 169.830 0.141 0.509 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1286 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.5%. 99: The balanceable part of the MD step is 53%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.009 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 155.789 0.154 0.555 0.027 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.4%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.2%. 99: 99: 99: NOTE: 45 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 197.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 229.470 0.105 0.377 0.040 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.9%. 99: The balanceable part of the MD step is 45%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 236.809 0.101 0.365 0.041 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.4%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.1%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 174.343 0.138 0.496 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.8%. 99: The balanceable part of the MD step is 43%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 161.105 0.149 0.536 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 3.3%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 170.557 0.141 0.507 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1297 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 170.997 0.140 0.505 0.030 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 222.384 0.108 0.389 0.039 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 240.756 0.100 0.359 0.042 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 174.516 0.138 0.495 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 164.660 0.146 0.525 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 168.832 0.142 0.512 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1295 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 168.848 0.142 0.512 0.029 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 239.870 0.100 0.360 0.042 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 197.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 238.931 0.100 0.362 0.041 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 144.491 0.166 0.598 0.025 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.009 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 157.647 0.152 0.548 0.027 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.010 187.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 154.591 0.155 0.559 0.027 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1406 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 161.577 0.149 0.535 0.028 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 204.950 0.117 0.422 0.036 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 208.703 0.115 0.414 0.036 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 165.929 0.145 0.521 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 163.203 0.147 0.529 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 187.603 0.128 0.461 0.033 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1322 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 165.971 0.145 0.521 0.029 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 236.305 0.102 0.366 0.041 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 168.116 0.143 0.514 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 177.503 0.135 0.487 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 167.784 0.143 0.515 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 169.475 0.142 0.510 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1318 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 166.047 0.145 0.520 0.029 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.007 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 199.951 0.120 0.432 0.035 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 193.095 0.124 0.447 0.034 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 197.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 191.210 0.126 0.452 0.033 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 176.734 0.136 0.489 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.007 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 197.430 0.122 0.438 0.034 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1297 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 160.217 0.150 0.539 0.028 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 204.392 0.117 0.423 0.035 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 240.907 0.100 0.359 0.042 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 186.222 0.129 0.464 0.032 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 182.008 0.132 0.475 0.032 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 169.163 0.142 0.511 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1299 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.2%. 99: The balanceable part of the MD step is 60%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 148.239 0.162 0.583 0.026 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.6%. 99: The balanceable part of the MD step is 59%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 211.243 0.114 0.409 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.8%. 99: The balanceable part of the MD step is 52%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.9%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 197.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 229.236 0.105 0.377 0.040 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB got disabled because it was unsuitable to use. 99: Average load imbalance: 4.4%. 99: The balanceable part of the MD step is 52%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 2.3%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.009 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 154.705 0.155 0.558 0.027 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.8%. 99: The balanceable part of the MD step is 54%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.0%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 154.154 0.156 0.560 0.027 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 3.3%. 99: The balanceable part of the MD step is 51%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 142.886 0.168 0.605 0.025 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1318 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.4%. 99: The balanceable part of the MD step is 62%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.2%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 158.766 0.151 0.544 0.028 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 3.0%. 99: The balanceable part of the MD step is 56%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 197.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 213.092 0.113 0.405 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.5%. 99: The balanceable part of the MD step is 57%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 197.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 235.501 0.102 0.367 0.041 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 55%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 166.999 0.144 0.517 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.0%. 99: The balanceable part of the MD step is 49%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.0%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 150.709 0.159 0.573 0.026 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.9%. 99: The balanceable part of the MD step is 55%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 167.319 0.143 0.516 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1314 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 149.718 0.160 0.577 0.026 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 218.993 0.110 0.395 0.038 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 196.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 226.064 0.106 0.382 0.039 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 176.757 0.136 0.489 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 177.480 0.135 0.487 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 175.568 0.137 0.492 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1319 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 197.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 162.613 0.148 0.531 0.028 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 196.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 198.851 0.121 0.434 0.035 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 197.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 212.025 0.113 0.407 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 176.754 0.136 0.489 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 152.401 0.157 0.567 0.026 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 174.826 0.137 0.494 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1299 ms) 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (17079 ms total) 99: 99: [----------] Global test environment tear-down 99: [==========] 13 tests from 1 test suite ran. (17093 ms total) 99: [ PASSED ] 13 tests. 99/104 Test #99: MdrunCoordinationConstraintsTests2Ranks ... Passed 17.11 sec test 100 Start 100: MdrunFEPTests 100: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunFEPTests.xml" 100: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 100: Test timeout computed to be: 600 100: [==========] Running 14 tests from 2 test suites. 100: [----------] Global test environment set-up. 100: [----------] 2 tests from ExpandedEnsembleTest 100: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 16 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.034 0.017 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 87.348 0.275 0.989 0.036 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 100: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 100: 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.023 0.011 199.2 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 68.822 0.349 1.255 0.029 100: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (54 ms) 100: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 1 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.018 0.009 199.5 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 18.969 1.265 4.555 0.008 100: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (23 ms) 100: [----------] 2 tests from ExpandedEnsembleTest (78 ms total) 100: 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -34838 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.062 0.031 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 58.681 0.409 1.472 0.120 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (276 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 2080309111 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.059 0.029 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 61.668 0.389 1.401 0.126 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (117 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -419692561 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.048 0.024 199.4 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 74.682 0.321 1.157 0.153 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (105 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 155]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 155]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to -1076629629 100: 100: Generated 171 of the 171 non-bonded parameter combinations 100: 100: Generated 171 of the 171 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 358.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 1 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.96 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.051 0.025 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 71.409 0.336 1.210 0.147 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (220 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 165]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 165]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to -672002 100: 100: Generated 190 of the 190 non-bonded parameter combinations 100: 100: Generated 190 of the 190 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'CL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'CL' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 361.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 2 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.96 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.049 0.025 199.5 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 73.446 0.327 1.176 0.152 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (39 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 100: and vdw_modifier=Force-switch 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 100 steps, 0.1 ps. 100: Setting the LD random seed to -29123089 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.224 0.112 199.9 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 77.898 0.308 1.109 0.160 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (197 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There were 11 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -845251477 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.082 0.041 199.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 44.154 0.544 1.957 0.090 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (124 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: Removing center of mass motion in the presence of position restraints 100: might cause artifacts. When you are using position restraints to 100: equilibrate a macro-molecule, the artifacts are usually negligible. 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There were 11 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -1344278529 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.081 0.040 199.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 44.838 0.535 1.927 0.092 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (124 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -4327169 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.88 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.039 0.019 199.4 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 93.869 0.256 0.920 0.192 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (108 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: There was 1 NOTE 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.020 0.010 198.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 179.396 0.134 0.482 0.368 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to 1979580409 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.88 100: 100: This run will generate roughly 0 Mb of data 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (101 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -68300818 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.058 0.029 199.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 62.193 0.386 1.389 0.127 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (117 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 1995335167 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.88 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.037 0.019 199.5 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 97.557 0.246 0.886 0.200 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (96 ms) 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (1631 ms total) 100: 100: [----------] Global test environment tear-down 100: [==========] 14 tests from 2 test suites ran. (1737 ms total) 100: [ PASSED ] 14 tests. 100/104 Test #100: MdrunFEPTests ............................. Passed 1.75 sec test 101 Start 101: MdrunPullTests 101: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunPullTests.xml" 101: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 101: Test timeout computed to be: 600 101: [==========] Running 4 tests from 1 test suite. 101: [----------] Global test environment set-up. 101: [----------] 4 tests from PullTest/PullIntegrationTest 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.600 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.032 0.016 199.4 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 113.710 0.211 0.760 0.853 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (229 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.301 nm 0.400 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.035 0.018 199.4 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 102.173 0.235 0.846 0.766 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (217 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Pull group 3 'r_3' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1292.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.357 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.500 nm 101: 1 3 2 101: 3 3 8 0.331 nm 0.400 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.034 0.017 199.5 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 106.749 0.225 0.809 0.801 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (225 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.000 nm 101: 0.050 nm 0.000 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.031 0.015 199.4 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 117.191 0.205 0.737 0.879 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (224 ms) 101: [----------] 4 tests from PullTest/PullIntegrationTest (896 ms total) 101: 101: [----------] Global test environment tear-down 101: [==========] 4 tests from 1 test suite ran. (910 ms total) 101: [ PASSED ] 4 tests. 101/104 Test #101: MdrunPullTests ............................ Passed 0.92 sec test 102 Start 102: MdrunRotationTests 102: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunRotationTests.xml" 102: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 102: Test timeout computed to be: 600 102: [==========] Running 12 tests from 1 test suite. 102: [----------] Global test environment set-up. 102: [----------] 12 tests from RotationWorks/RotationTest 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 102: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: trr version: GMX_trn_file (single precision) 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1633974535 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 376.695 0.064 0.459 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (18 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 102: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 401467315 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.021 0.011 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 425.924 0.056 0.406 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (15 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 102: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -637749265 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.010 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 460.051 0.052 0.376 0.011 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (14 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 102: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1614875173 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.021 0.010 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 430.114 0.056 0.402 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (15 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 102: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 2077978855 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.010 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 468.004 0.051 0.369 0.011 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (14 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 102: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1359151105 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.020 0.010 198.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 450.311 0.053 0.384 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (14 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 102: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 2044722878 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.018 0.009 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 489.968 0.049 0.353 0.011 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (13 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 102: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1168801802 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.010 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 464.256 0.052 0.372 0.011 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (14 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 102: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -476371893 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.022 0.011 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 409.727 0.059 0.422 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (15 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 102: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -138940417 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.023 0.011 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 397.229 0.060 0.435 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (16 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 102: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -4751363 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.020 0.010 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 446.259 0.054 0.387 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (14 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 102: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1007829137 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 376.748 0.064 0.459 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (16 ms) 102: [----------] 12 tests from RotationWorks/RotationTest (185 ms total) 102: 102: [----------] Global test environment tear-down 102: [==========] 12 tests from 1 test suite ran. (199 ms total) 102: [ PASSED ] 12 tests. 102/104 Test #102: MdrunRotationTests ........................ Passed 0.21 sec test 103 Start 103: MdrunSimulatorComparison 103: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 103: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 103: Test timeout computed to be: 600 103: [==========] Running 0 tests from 0 test suites. 103: [==========] 0 tests from 0 test suites ran. (0 ms total) 103: [ PASSED ] 0 tests. 103: 103: YOU HAVE 82 DISABLED TESTS 103: 103/104 Test #103: MdrunSimulatorComparison .................. Passed 0.01 sec test 104 Start 104: MdrunVirtualSiteTests 104: Test command: /build/reproducible-path/gromacs-2026.1/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 104: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests 104: Test timeout computed to be: 600 104: [==========] Running 37 tests from 2 test suites. 104: [----------] Global test environment set-up. 104: [----------] 1 test from VirtualSiteVelocityTest 104: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 104: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 104: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 104: 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 1.8%. 104: The balanceable part of the MD step is 44%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.8%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.020 0.010 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 79.087 0.303 1.092 0.022 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: trr version: GMX_trn_file (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (15 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 2.1%. 104: The balanceable part of the MD step is 47%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 1.0%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.018 0.009 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 85.647 0.280 1.009 0.024 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (14 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 6.4%. 104: The balanceable part of the MD step is 40%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 2.6%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.008 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 93.091 0.258 0.928 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (13 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 91.104 0.263 0.948 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 199.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 89.118 0.269 0.970 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (16 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 91.237 0.263 0.947 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (16 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.008 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 92.391 0.260 0.935 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (16 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.008 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 92.668 0.259 0.932 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (16 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 96.065 0.250 0.899 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (16 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 2.5%. 104: The balanceable part of the MD step is 45%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 1.2%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 98.080 0.245 0.881 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (13 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 1.8%. 104: The balanceable part of the MD step is 40%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.7%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.015 0.007 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 103.985 0.231 0.831 0.029 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (12 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.4 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 98.888 0.243 0.874 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.015 0.008 198.3 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 100.012 0.240 0.864 0.028 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (19 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.008 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 92.965 0.258 0.929 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 94.321 0.254 0.916 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (20 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.7 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 97.699 0.246 0.884 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 198.6 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 90.656 0.265 0.953 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (22 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.015 0.007 198.6 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 105.321 0.228 0.820 0.029 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (19 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.015 0.007 198.6 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 103.683 0.231 0.833 0.029 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (20 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.018 0.009 199.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 87.603 0.274 0.986 0.024 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (22 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.020 0.010 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 75.908 0.316 1.138 0.021 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.1-Debian_2026.1_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (22 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (372 ms total) 104: 104: [----------] Global test environment tear-down 104: [==========] 37 tests from 2 test suites ran. (386 ms total) 104: [ PASSED ] 37 tests. 104/104 Test #104: MdrunVirtualSiteTests ..................... Passed 0.40 sec 100% tests passed, 0 tests failed out of 104 Label Time Summary: GTest = 136.50 sec*proc (97 tests) IntegrationTest = 56.16 sec*proc (30 tests) MpiTest = 87.24 sec*proc (24 tests) QuickGpuTest = 24.56 sec*proc (25 tests) SlowGpuTest = 96.02 sec*proc (15 tests) SlowTest = 68.30 sec*proc (14 tests) UnitTest = 12.04 sec*proc (53 tests) Total Test time (real) = 103.24 sec /usr/bin/make -j6 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.1 -B/build/reproducible-path/gromacs-2026.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.1 -B/build/reproducible-path/gromacs-2026.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic-dp/CMakeFiles 76 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" gtest make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wundef -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-declarations -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.1-Debian_2026.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.1/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.1-1 -P /build/reproducible-path/gromacs-2026.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend [ 0%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build [ 1%] Built target release-version-info [ 1%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 3%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 3%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build [ 5%] Built target tng_io_obj /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fmm/CMakeFiles/fmm.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 6%] Built target fmm /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/DependInfo.cmake "--color=" mpithreads [ 7%] Built target linearalgebra /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/DependInfo.cmake "--color=" sync_cyclecount make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/main.cpp.o -MF CMakeFiles/mpithreads.dir/main.cpp.o.d -o CMakeFiles/mpithreads.dir/main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/main.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build [ 7%] Built target h5md make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -MF CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o.d -o CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/sync_cyclecount.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/DependInfo.cmake "--color=" mpi_speedtest [ 7%] Built target options cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/reduce.cpp.o -MF CMakeFiles/mpithreads.dir/reduce.cpp.o.d -o CMakeFiles/mpithreads.dir/reduce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/reduce.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -MF CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/mpi_speedtest.cpp [ 10%] Built target colvars_objlib /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/notmpi.dir/DependInfo.cmake "--color=" notmpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/notmpi.dir/notmpi.cpp.o -MF CMakeFiles/notmpi.dir/notmpi.cpp.o.d -o CMakeFiles/notmpi.dir/notmpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/notmpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -MF CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/send_recv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/sync_cyclecount.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/once.cpp.o -MF CMakeFiles/mpithreads.dir/once.cpp.o.d -o CMakeFiles/mpithreads.dir/once.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/once.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sync_cyclecount.dir/link.d CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/sync_cyclecount make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 10%] Built target sync_cyclecount cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/send_recv.cpp.o -MF CMakeFiles/mpithreads.dir/send_recv.cpp.o.d -o CMakeFiles/mpithreads.dir/send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/send_recv.cpp /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build.make src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/DependInfo.cmake "--color=" alloc_check make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build.make src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/alloc_check.cpp.o -MF CMakeFiles/alloc_check.dir/alloc_check.cpp.o.d -o CMakeFiles/alloc_check.dir/alloc_check.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/alloc_check.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/multicast.cpp.o -MF CMakeFiles/mpithreads.dir/multicast.cpp.o.d -o CMakeFiles/mpithreads.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -MF CMakeFiles/mpi_speedtest.dir/multicast.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/alloc_check.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/notmpi.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alloc_check.dir/link.d CMakeFiles/alloc_check.dir/alloc_check.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/alloc_check make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 11%] Built target pulling /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis [ 11%] Built target alloc_check cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cond-var.cpp.o -MF CMakeFiles/mpithreads.dir/cond-var.cpp.o.d -o CMakeFiles/mpithreads.dir/cond-var.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/cond-var.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 11%] Built target energyanalysis /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/notmpi.dir/link.d CMakeFiles/notmpi.dir/notmpi.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/notmpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build [ 11%] Built target notmpi cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/atomic.cpp.o -MF CMakeFiles/mpithreads.dir/atomic.cpp.o.d -o CMakeFiles/mpithreads.dir/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/atomic.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 11%] Built target taskassignment /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cycles.cpp.o -MF CMakeFiles/mpithreads.dir/cycles.cpp.o.d -o CMakeFiles/mpithreads.dir/cycles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/cycles.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpi_speedtest.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/split.cpp.o -MF CMakeFiles/mpithreads.dir/split.cpp.o.d -o CMakeFiles/mpithreads.dir/split.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/test/split.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpi_speedtest.dir/link.d CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpi_speedtest make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 13%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 14%] Built target mpi_speedtest make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpithreads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpithreads.dir/link.d CMakeFiles/mpithreads.dir/main.cpp.o CMakeFiles/mpithreads.dir/reduce.cpp.o CMakeFiles/mpithreads.dir/once.cpp.o CMakeFiles/mpithreads.dir/send_recv.cpp.o CMakeFiles/mpithreads.dir/multicast.cpp.o "CMakeFiles/mpithreads.dir/cond-var.cpp.o" CMakeFiles/mpithreads.dir/atomic.cpp.o CMakeFiles/mpithreads.dir/cycles.cpp.o CMakeFiles/mpithreads.dir/split.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpithreads make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 14%] Built target mpithreads make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 63%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" nblib make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 64%] Built target gmxapi [ 65%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" argon-forces-integration make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" methane-water-integration make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 65%] Built target argon-forces-integration [ 65%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-soname,libgtest.so.1.17.0 -o ../../../../lib/libgtest.so.1.17.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 65%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googlemock /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" gmock make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wundef -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmock.dir/link.d -Wl,-soname,libgmock.so.1.17.0 -o ../../../../lib/libgmock.so.1.17.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.17.0 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 65%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/testutils /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake "--color=" testutils make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/conftest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/filematchers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o -MF CMakeFiles/testutils.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/interactivetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o -MF CMakeFiles/testutils.dir/loggertest.cpp.o.d -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/loggertest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o -MF CMakeFiles/testutils.dir/mpi_printer.cpp.o.d -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/mpi_printer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o -MF CMakeFiles/testutils.dir/mpitest.cpp.o.d -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/mpitest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DHAVE_OPEN_MEMSTREAM=1 -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/posixmemstream.cpp.o -MF CMakeFiles/testutils.dir/posixmemstream.cpp.o.d -o CMakeFiles/testutils.dir/posixmemstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/posixmemstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o -MF CMakeFiles/testutils.dir/refdata.cpp.o.d -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/refdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o -MF CMakeFiles/testutils.dir/refdata_xml.cpp.o.d -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/refdata_xml.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/setenv.cpp.o -MF CMakeFiles/testutils.dir/setenv.cpp.o.d -o CMakeFiles/testutils.dir/setenv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/setenv.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o -MF CMakeFiles/testutils.dir/simulationdatabase.cpp.o.d -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o -MF CMakeFiles/testutils.dir/stdiohelper.cpp.o.d -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/stdiohelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o -MF CMakeFiles/testutils.dir/stringtest.cpp.o.d -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/stringtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o -MF CMakeFiles/testutils.dir/testasserts.cpp.o.d -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testasserts.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o -MF CMakeFiles/testutils.dir/testfilemanager.cpp.o.d -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testfilemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o -MF CMakeFiles/testutils.dir/testfileredirector.cpp.o.d -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testfileredirector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o -MF CMakeFiles/testutils.dir/test_device.cpp.o.d -o CMakeFiles/testutils.dir/test_device.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/test_device.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -MF CMakeFiles/testutils.dir/test_hardware_environment.cpp.o.d -o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/test_hardware_environment.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o -MF CMakeFiles/testutils.dir/testinit.cpp.o.d -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testinit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o -MF CMakeFiles/testutils.dir/testmatchers.cpp.o.d -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testmatchers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o -MF CMakeFiles/testutils.dir/testoptions.cpp.o.d -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/testoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o -MF CMakeFiles/testutils.dir/textblockmatchers.cpp.o.d -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/textblockmatchers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/topologyhelpers.cpp.o -MF CMakeFiles/testutils.dir/topologyhelpers.cpp.o.d -o CMakeFiles/testutils.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -MF CMakeFiles/testutils.dir/tprfilegenerator.cpp.o.d -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tprfilegenerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/trajectoryreader.cpp.o -MF CMakeFiles/testutils.dir/trajectoryreader.cpp.o.d -o CMakeFiles/testutils.dir/trajectoryreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/trajectoryreader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o -MF CMakeFiles/testutils.dir/xvgtest.cpp.o.d -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/xvgtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/testutils -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -MF CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o.d -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/tinyxml2/tinyxml2.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/posixmemstream.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/setenv.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/topologyhelpers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/trajectoryreader.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 67%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake "--color=" mdrun_test_infrastructure make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake "--color=" nblib_test_infrastructure make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake "--color=" testutils-test make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake "--color=" testutils-mpi-test make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/DependInfo.cmake "--color=" mpicomm-test make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake "--color=" utility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/energyreader.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/interactivetest.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/testsystems.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/mpitest.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o -MF CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o.d -o CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/mpicomm.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/naming.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 67%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/posixmemstream.cpp.o -MF CMakeFiles/testutils-test.dir/posixmemstream.cpp.o.d -o CMakeFiles/testutils-test.dir/posixmemstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/posixmemstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpicomm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpicomm-test.dir/link.d "CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o" "CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mpicomm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 67%] Built target mpicomm-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/refdata_tests.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" utility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o -MF CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/coordinate_exception_handling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 67%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o" "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 67%] Built target utility-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/bitmask32.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" mdlib-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/posixmemstream.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 67%] Built target testutils-test /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" density_fitting_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -MF CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o.d -o CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constraintgroupsize.cpp /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 68%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" qmmm_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/energydrifttracker.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" colvars_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmforceproviderstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 68%] Built target density_fitting_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/fixedcapacityvector.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" plumed_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 68%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" plumed_md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 68%] Built target plumed_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 68%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 68%] Built target plumed_md-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/message_string_collector.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 69%] Built target awh-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" nnpot_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mpicomm.cpp.o -MF CMakeFiles/utility-test.dir/mpicomm.cpp.o.d -o CMakeFiles/utility-test.dir/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/path.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" listed_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 69%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" nbnxm-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests/pairs.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" nbnxm-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 71%] Built target nnpot_applied_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 71%] Built target nbnxm-gpu-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -MF CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o.d -o CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/plainpairlist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/testsystem.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" nonbonded-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 71%] Built target nbnxm-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/txtdump.cpp.o -MF CMakeFiles/utility-test.dir/txtdump.cpp.o.d -o CMakeFiles/utility-test.dir/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/txtdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 71%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/DependInfo.cmake "--color=" nonbonded-fep-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/tests/freeenergygpukernel.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vecdump.cpp.o -MF CMakeFiles/utility-test.dir/vecdump.cpp.o.d -o CMakeFiles/utility-test.dir/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/vecdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" onlinehelp-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-gpu-test.dir/link.d "CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o" "CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 71%] Built target nonbonded-fep-gpu-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vectypes.cpp.o -MF CMakeFiles/utility-test.dir/vectypes.cpp.o.d -o CMakeFiles/utility-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" domdec-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/vsite.cpp.o -MF CMakeFiles/mdlib-test.dir/vsite.cpp.o.d -o CMakeFiles/mdlib-test.dir/vsite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/vsite.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 71%] Built target nonbonded-fep-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 71%] Built target onlinehelp-test-shared cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/mdgpugraph.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" domdec-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" ewald-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/mpicomm.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/txtdump.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/vecdump.cpp.o" "CMakeFiles/utility-test.dir/vectypes.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 72%] Built target utility-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" fft-test [ 72%] Built target domdec-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmegathertest.cpp /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/DependInfo.cmake "--color=" fmm-interface-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmm_mdpoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/vsite.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 73%] Built target mdlib-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 73%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 73%] Built target fft-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/tests/fmmforceproviderbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pme.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/DependInfo.cmake "--color=" gpu_utils-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o -MF CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o.d -o CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fmm-interface-tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fmm-interface-tests.dir/link.d "CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o" "CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fmm-interface-tests ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 73%] Built target fmm-interface-tests cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-mpi-test.dir/link.d "CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o" "CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 73%] Built target gpu_utils-mpi-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/boxmatrix.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 75%] Built target ewald-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/complex.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/coordinatetransformation.cpp /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 75%] Built target mdrunutility-test-shared cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/extents.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 75%] Built target hardware-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" mdtypes-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/exponentialmovingaverage.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 75%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdspan/tests/mdspan.cpp /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" options-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 75%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" pbcutil-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/filenameoption.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/com.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 76%] Built target mdspan-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/tests/pbcenums.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 76%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/gammadistribution.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 76%] Built target mdtypes-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/optimization.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/seed.cpp /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/DependInfo.cmake "--color=" serialization-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 76%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/serialization-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/serialization-test.dir/link.d "CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/serialization-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 77%] Built target serialization-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 77%] Built target table-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" timing-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/timing/tests/timing.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 78%] Built target taskassignment-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/atoms.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 80%] Built target options-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/base.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 80%] Built target random-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 80%] Built target timing-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/generate_test_points.cpp.o -MF CMakeFiles/simd-test.dir/generate_test_points.cpp.o.d -o CMakeFiles/simd-test.dir/generate_test_points.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/generate_test_points.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/scalar.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/compat/tests/pointers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 80%] Built target pull-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/scalar_util.cpp /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 80%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -MF CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmxanatestbase.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/index.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_floatingpoint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 81%] Built target math-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 81%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_integer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 82%] Built target topology-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_memory.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 84%] Built target gmxana-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" correlations-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 85%] Built target pdb2gmx2-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" analysisdata-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/simd/tests/simd4_vector_operations.cpp [ 85%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 86%] Built target correlations-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/generate_test_points.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 86%] Built target simd-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" tool-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/helpwriting.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 86%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" tool-test-with-leaks make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/trjconv.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 86%] Built target tool-test-with-leaks cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 86%] Built target analysisdata-test-shared cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/readir.cpp /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/DependInfo.cmake "--color=" h5md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o -MF CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o.d -o CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md/tests/h5md_disabled.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/h5md-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/setbothtime.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/h5md-test.dir/link.d "CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o" "CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/h5md.dir/h5md.cpp.o -o ../../../../../bin/h5md-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 86%] Built target h5md-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/settimestep.cpp /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/topdirs.cpp /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/indexutil.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 86%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" mdrun-output-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 88%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/helpwriting.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/interactiveMD.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 88%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/filetypes.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/mimic.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/awh.cpp.o -MF CMakeFiles/mdrun-test.dir/awh.cpp.o.d -o CMakeFiles/mdrun-test.dir/awh.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/awh.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multiple_time_stepping.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 89%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" mdrun-single-rank-algorithms-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 89%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target mdrun-single-rank-algorithms-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/timecontrol.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" minimize-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/tngio.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -MF CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o.d -o CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/xdr_serializer.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/tpitest.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" mdrun-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target minimize-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/boxdeformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/rerun.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" mdrun-multisim-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/awh.cpp.o" "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target mdrun-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/simple_mdrun.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-equivalence-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/replicaexchange_equivalence.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" mdrun-mpi-pme-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target mdrun-multisim-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 90%] Built target fileio-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" mdrun-coordination-basic-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 92%] Built target mdrun-non-integrator-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" mdrun-coordination-coupling-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 92%] Built target mdrun-multisim-replex-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" mdrun-coordination-constraints-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 92%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" mdrun-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/expandedensemble.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 92%] Built target mdrun-coordination-basic-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" mdrun-pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 92%] Built target mdrun-multisim-replex-equivalence-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 93%] Built target mdrun-coordination-constraints-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" mdrun-rotation-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/pull_rotation.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" mdrun-simulator-comparison-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/simulator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 93%] Built target mdrun-coordination-coupling-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" mdrun-vsites-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/tests/virtualsites.cpp /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" gmxapi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 93%] Built target mdrun-fep-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" workflow-details-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 93%] Built target mdrun-pull-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" nblib-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 93%] Built target mdrun-rotation-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 93%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 94%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" nblib-setup-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 94%] Built target mdrun-vsites-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" nblib-tpr-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" nblib-integration-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 94%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/nbkernelsystem.cpp /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" nblib-listed-forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/helpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target gmxapi-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib/util/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" nblib-util-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/topology.cpp /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/typetests.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -MF CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/plainpairlistranges.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" analysisdata-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target nblib-setup-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/arraydata.cpp /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/average.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" nblib-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 96%] Built target nblib-tests cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.1/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/nblib/tests -I/build/reproducible-path/gromacs-2026.1/api/nblib/include -I/build/reproducible-path/gromacs-2026.1/api/nblib -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 97%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 97%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/msd.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [ 98%] Built target commandline-test cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/testutils/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' cd /build/reproducible-path/gromacs-2026.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp /build/reproducible-path/gromacs-2026.1/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.1/build/basic-dp/lib ctest -V ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2026.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2026.1/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2026.1/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -19484821 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.064 0.032 199.4 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 15.836 1.516 10.656 0.001 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (357 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -875072526 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.022 0.011 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 45.543 0.527 3.705 0.002 1: [ OK ] GmxApiTest.RunnerBasicMD (308 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -201459273 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.026 0.013 199.3 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 274.013 0.088 0.616 0.013 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.021 0.010 199.3 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 342.155 0.070 0.493 0.016 1: [ OK ] GmxApiTest.RunnerReinitialize (336 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 2079194590 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.020 0.010 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 51.572 0.465 3.272 0.002 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.018 0.009 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 56.043 0.428 3.011 0.003 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (324 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -67277061 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.023 0.012 199.3 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 72.012 0.333 2.343 0.003 1: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.020 0.010 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 33.614 0.714 5.020 0.002 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (318 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -1518538788 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (269 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (1916 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (1931 ms total) 1: [ PASSED ] 9 tests. 1/104 Test #1: GmxapiExternalInterfaceTests .............. Passed 1.95 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -606453762 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (290 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -869377 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (248 ms) 2: [----------] 2 tests from GmxApiTest (538 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (551 ms total) 2: [ PASSED ] 2 tests. 2/104 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.56 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (17 ms) 3: [----------] 8 tests from NBlibTest (18 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (0 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (0 ms) 3: [----------] 1 test from LinearChainDataFixture (0 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (20 ms total) 3: [ PASSED ] 44 tests. 3/104 Test #3: NbLibListedForcesTests .................... Passed 0.03 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/104 Test #4: NbLibSamplesTestArgon ..................... Passed 0.01 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/104 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.01 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/104 Test #6: NbLibUtilTests ............................ Passed 0.01 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (1 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (2 ms total) 7: [ PASSED ] 57 tests. 7/104 Test #7: NbLibSetupTests ........................... Passed 0.03 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (4 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (4 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (3 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (5 ms) 8: [----------] 4 tests from TprReaderTest (16 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (31 ms total) 8: [ PASSED ] 4 tests. 8/104 Test #8: NbLibTprTests ............................. Passed 0.04 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (4 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (4 ms total) 9: [ PASSED ] 20 tests. 9/104 Test #9: NbLibIntegrationTests ..................... Passed 0.02 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/104 Test #10: NbLibIntegratorTests ...................... Passed 0.01 sec test 11 Start 11: threadMPI-mpithreads 11: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mpithreads "-nt" "3" 11: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test 11: Test timeout computed to be: 1500 11: 11: thread_mpi tester. 11: 11: Number of threads: 3 11: 11: thread 0: got arg 10; total number of hw threads: 16 11: my rank = 0 11: Setting thread affinity 11: thread 2: got arg 10; total number of hw threads: 16 11: my rank = 2 11: thread 1: got arg 10; total number of hw threads: 16 11: my rank = 1 11: Testing atomic functions.. 11: OK. 11: Starting tMPI_Thread_cond_signal test: 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 1: 12 11: processed by thread 2: 988 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 468 11: processed by thread 2: 532 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 501 11: processed by thread 1: 499 11: 11: Starting tMPI_Thread_cond_broadcast test: 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 1: 804 11: processed by thread 2: 1196 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 1118 11: processed by thread 2: 882 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 1050 11: processed by thread 1: 950 11: 11: 11: sizeof(atomic_t) = 64, sizeof(atomic_t_ptr)=64, sizeof(spinlock)=64 11: Testing spinlocks.. 11: OK. 11: 11: Testing locks.. 11: OK. 11: 11: Barrier data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Starting MPI_Send and MPI_Recv tests 11: Received: 'From thread 1 to 0: hello.' 11: Received: 'From thread 2 to 0: hello.' 11: Received: 'From thread 1 to 1: hello.' 11: Received: 'From thread 2 to 1: hello.' 11: 11: Starting MPI_Sendrecv tests 11: Received: 'Sendrecv hello, from thread 1' 11: Received: 'Sendrecv hello, from thread 2' 11: Received: 'Sendrecv hello, from thread 0' 11: 11: Starting MPI_Isend/MPI_Irecv tests 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Split test 11: I'm in world rank 1, and have new rank 0 in group 0x7f03d4008960 of size 1 11: I'm in world rank 0, and have new rank 1 in group 0x7f03d4007b00 of size 2 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0x7f03d4007b00 of size 2 11: I'm in world rank 1, and have new rank 0 in group 0x7f03d4009350 of size 1 11: my rank is 1, MPI_Comm_compare said: 3 11: I'm in world rank 0, and have new rank 0 in group 0x7f03d4008960 of size 1 11: my rank is 0, MPI_Comm_compare said: 3 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0x7f03d4009c10 of size 1 11: my rank is 2, MPI_Comm_compare said: 3 11: I'm in world rank 1, and have new rank 1 in group 0x7f03d4009350 of size 3 11: my rank is 1, MPI_Comm_compare said: 2 11: I'm in world rank 2, and have new rank 0 in group 0x7f03d4009350 of size 3 11: my rank is 2, MPI_Comm_compare said: 2 11: I'm in world rank 0, and have new rank 2 in group 0x7f03d4009350 of size 3 11: my rank is 0, MPI_Comm_compare said: 2 11: Starting repeated MPI_Split() test. 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: Done. 11: 11: Starting MPI_Bcast test 11: Received: 'Broadcast message 0 from 0' 11: Received: 'Broadcast message 0 from 1' 11: Received: 'Broadcast message 0 from 2' 11: Received: 'Broadcast message 1 from 0' 11: Received: 'Broadcast message 1 from 1' 11: Received: 'Broadcast message 1 from 2' 11: Broadcast data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Gather test 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Gather data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Gatherv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Scatter test 11: Received from 0: 'Scatter message from 000 to 000' 11: Received back from 1: 'Scatter message from 000 to 001' 11: Received back from 2: 'Scatter message from 000 to 002' 11: Scatter data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Scatterv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Alltoall test 11: From 0: 0->0(0) 1->0(0) 2->0(0) 11: From 1: 0->1(0) 1->1(0) 2->1(0) 11: From 2: 0->2(0) 1->2(0) 2->2(0) 11: From 0: 0->0(1) 1->0(1) 2->0(1) 11: From 1: 0->1(1) 1->1(1) 2->1(1) 11: From 2: 0->2(1) 1->2(1) 2->2(1) 11: From 0: 0->0(2) 1->0(2) 2->0(2) 11: From 1: 0->1(2) 1->1(2) 2->1(2) 11: From 2: 0->2(2) 1->2(2) 2->2(2) 11: From 0: 0->0(3) 1->0(3) 2->0(3) 11: From 1: 0->1(3) 1->1(3) 2->1(3) 11: From 2: 0->2(3) 1->2(3) 2->2(3) 11: Alltoallv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Reduce test 11: again: my rank = 0 11: again: my rank = 2 11: Results from mpi_reduce: 11: (0: 2 == 2): OK 11: (1: 5 == 5): OK 11: (2: 8 == 8): OK 11: (3: 11 == 11): OK 11: (4: 14 == 14): OK 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 1 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 1: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 2: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 1: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 2: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Scan test 11: Results from mpi_scan process 0: 11: OK 11: again: my rank = 0 11: again: my rank = 2 11: again: my rank = 1 11: Printing this number once: 0 (my rank=1) 11: 11: Starting tMPI_Once test 11: Printing this number once: 1 (my rank=2) 11: Printing this number once: 2 (my rank=0) 11: Printing this number once: 3 (my rank=2) 11: Printing this number once: 4 (my rank=2) 11: Printing this number once: 5 (my rank=2) 11: Printing this number once: 6 (my rank=2) 11: Printing this number once: 7 (my rank=0) 11: Printing this number once: 8 (my rank=0) 11: Printing this number once: 9 (my rank=0) 11: I was first for 0, my rank=1 11: Done. 11: 11: Finishing.. 11/104 Test #11: threadMPI-mpithreads ...................... Passed 11.01 sec test 12 Start 12: threadMPI-sync_cyclecount 12: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/sync_cyclecount "2" "0" "1" 12: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test 12: Test timeout computed to be: 1500 12: 12: sync_cyclecount. 12: 12: Number of threads: 3 12: 12: Number of counters: 3 12: 12: No cycle count. 12/104 Test #12: threadMPI-sync_cyclecount ................. Passed 0.00 sec test 13 Start 13: threadMPI-mpi_speedtest 13: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mpi_speedtest "-nt" "3" 13: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test 13: Test timeout computed to be: 1500 13: Starting Thread 2: 13: Starting Thread 1: 13: Starting Thread 0: 13: Async data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Broadcast data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Gather data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Scatter data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Scatterv data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Alltoallv data test: 13: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13: OK. 13: Thread 0: 1.52964e+10 cycles 13: Thread 2: 1.52964e+10 cycles 13: Thread 1: 1.52964e+10 cycles 13/104 Test #13: threadMPI-mpi_speedtest ................... Passed 7.29 sec test 14 Start 14: threadMPI-notmpi 14: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/notmpi "-nt" "3" 14: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test 14: Test timeout computed to be: 1500 14: 14: notmpi. 14: 14: Number of threads: 3 14: 14: This platform supports setting thread affinity 14: My ID=1, i=1000, tid=0x7f16cc000be0 14: My ID=2, i=1000, tid=0x7f16cc000be0 14: My ID=0, i=1000, tid=0x55927e4025f0 14: Total count: 3000 14/104 Test #14: threadMPI-notmpi .......................... Passed 0.00 sec test 15 Start 15: threadMPI-alloc_check 15: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/alloc_check "-nt" "3" 15: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/external/thread_mpi/test 15: Test timeout computed to be: 1500 15: 15: Memory (de)allocation tester. 15: 15: Number of threads: 3 15: 15: thread 2: got arg 10; total number of hw threads: 16 15: thread 0: got arg 10; total number of hw threads: 16 15: thread 1: got arg 10; total number of hw threads: 16 15: my rank = 1 15: my rank = 0 15: my rank = 2 15: 15: Starting MPI_Sendrecv tests 15: Received: 'Sendrecv hello, from thread 1' 15: Received: 'Sendrecv hello, from thread 2' 15: Received: 'Sendrecv hello, from thread 0' 15: 15: Starting MPI_Bcast test 15: Received: 'Broadcast message 0 from 0' 15: Received: 'Broadcast message 0 from 1' 15: Received: 'Broadcast message 0 from 2' 15: Received: 'Broadcast message 1 from 0' 15: Received: 'Broadcast message 1 from 1' 15: Received: 'Broadcast message 1 from 2' 15: 15: Starting MPI_Gather test 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Finishing.. 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15/104 Test #15: threadMPI-alloc_check ..................... Passed 0.00 sec test 16 Start 16: TestUtilsUnitTests 16: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests 16: Test timeout computed to be: 30 16: [==========] Running 81 tests from 8 test suites. 16: [----------] Global test environment set-up. 16: [----------] 10 tests from InteractiveTestHelperTest 16: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 16: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 16: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 16: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 16: 16: [----------] 10 tests from NameOfTestFromTupleTest 16: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 16: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 16: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 16: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 16: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 16: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 16: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 16: 16: [----------] 3 tests from RefDataFilenameMakerTest 16: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 16: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 16: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 16: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 16: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 16: 16: [----------] 6 tests from PosixMemstreamTest 16: [ RUN ] PosixMemstreamTest.ConstructsAndDestructs 16: [ OK ] PosixMemstreamTest.ConstructsAndDestructs (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilClosed 16: [ OK ] PosixMemstreamTest.HasAStreamUntilClosed (0 ms) 16: [ RUN ] PosixMemstreamTest.CanFetchString 16: [ OK ] PosixMemstreamTest.CanFetchString (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilStringIsFetched 16: [ OK ] PosixMemstreamTest.HasAStreamUntilStringIsFetched (0 ms) 16: [ RUN ] PosixMemstreamTest.CanWriteToStream 16: [ OK ] PosixMemstreamTest.CanWriteToStream (0 ms) 16: [ RUN ] PosixMemstreamTest.CanCheckBufferWithContents 16: [ OK ] PosixMemstreamTest.CanCheckBufferWithContents (0 ms) 16: [----------] 6 tests from PosixMemstreamTest (0 ms total) 16: 16: [----------] 37 tests from ReferenceDataTest 16: [ RUN ] ReferenceDataTest.HandlesSimpleData 16: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 16: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 16: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringBlockData 16: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesVectorData 16: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceData 16: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectData 16: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 16: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingData 16: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedData 16: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnys 16: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 16: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 16: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 16: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 16: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 16: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 16: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 16: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 16: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesReadingValues 16: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 16: [----------] 37 tests from ReferenceDataTest (4 ms total) 16: 16: [----------] 7 tests from FloatingPointDifferenceTest 16: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 16: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 16: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 16: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 16: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 16: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 16: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 16: 16: [----------] 4 tests from FloatingPointToleranceTest 16: [ RUN ] FloatingPointToleranceTest.UlpTolerance 16: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 16: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 16: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 16: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 16: 16: [----------] 4 tests from XvgTests 16: [ RUN ] XvgTests.CreateFile 16: [ OK ] XvgTests.CreateFile (0 ms) 16: [ RUN ] XvgTests.CheckMissing 16: [ OK ] XvgTests.CheckMissing (0 ms) 16: [ RUN ] XvgTests.CheckExtra 16: [ OK ] XvgTests.CheckExtra (0 ms) 16: [ RUN ] XvgTests.ReadIncorrect 16: [ OK ] XvgTests.ReadIncorrect (0 ms) 16: [----------] 4 tests from XvgTests (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 81 tests from 8 test suites ran. (7 ms total) 16: [ PASSED ] 81 tests. 16/104 Test #16: TestUtilsUnitTests ........................ Passed 0.02 sec test 17 Start 17: TestUtilsMpiUnitTests 17: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/testutils/tests 17: Test timeout computed to be: 30 17: [==========] Running 3 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 1 test from MpiSelfTest 17: [ RUN ] MpiSelfTest.Runs 17: [ OK ] MpiSelfTest.Runs (0 ms) 17: [----------] 1 test from MpiSelfTest (0 ms total) 17: 17: [----------] 2 tests from MpiRefDataTest 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank (0 ms) 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName (0 ms) 17: [----------] 2 tests from MpiRefDataTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 3 tests from 2 test suites ran. (1 ms total) 17: [ PASSED ] 3 tests. 17/104 Test #17: TestUtilsMpiUnitTests ..................... Passed 0.01 sec test 18 Start 18: UtilityUnitTests 18: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 18: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests 18: Test timeout computed to be: 30 18: [==========] Running 495 tests from 68 test suites. 18: [----------] Global test environment set-up. 18: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/0.Comparison 18: [ OK ] AllocatorTest/0.Comparison (0 ms) 18: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.Move 18: [ OK ] AllocatorTest/0.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/0 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/1.Comparison 18: [ OK ] AllocatorTest/1.Comparison (0 ms) 18: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.Move 18: [ OK ] AllocatorTest/1.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/1 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/2.Comparison 18: [ OK ] AllocatorTest/2.Comparison (0 ms) 18: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.Move 18: [ OK ] AllocatorTest/2.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/2 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/3.Comparison 18: [ OK ] AllocatorTest/3.Comparison (0 ms) 18: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.Move 18: [ OK ] AllocatorTest/3.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/3 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/4.Comparison 18: [ OK ] AllocatorTest/4.Comparison (0 ms) 18: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.Move 18: [ OK ] AllocatorTest/4.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/4 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator,gmx::PageAlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/5.Comparison 18: [ OK ] AllocatorTest/5.Comparison (0 ms) 18: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.Move 18: [ OK ] AllocatorTest/5.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/5 (0 ms total) 18: 18: [----------] 1 test from AllocatorUntypedTest 18: [ RUN ] AllocatorUntypedTest.Comparison 18: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 18: [----------] 1 test from AllocatorUntypedTest (0 ms total) 18: 18: [----------] 4 tests from EmptyArrayRefTest 18: [ RUN ] EmptyArrayRefTest.IsEmpty 18: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 18: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 18: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 18: 18: [----------] 1 test from EmptyConstArrayRefTest 18: [ RUN ] EmptyConstArrayRefTest.IsEmpty 18: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 18: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 18: 18: [----------] 8 tests from BoolType 18: [ RUN ] BoolType.ImplicitConversion 18: [ OK ] BoolType.ImplicitConversion (0 ms) 18: [ RUN ] BoolType.FalseByDefault 18: [ OK ] BoolType.FalseByDefault (0 ms) 18: [ RUN ] BoolType.Assignment 18: [ OK ] BoolType.Assignment (0 ms) 18: [ RUN ] BoolType.Copy 18: [ OK ] BoolType.Copy (0 ms) 18: [ RUN ] BoolType.ArrayRefCanBeCreated 18: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 18: [ RUN ] BoolType.CanBeCastToBool 18: [ OK ] BoolType.CanBeCastToBool (0 ms) 18: [ RUN ] BoolType.HasSizeOfBool 18: [ OK ] BoolType.HasSizeOfBool (0 ms) 18: [ RUN ] BoolType.HasAlignmentOfBool 18: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 18: [----------] 8 tests from BoolType (0 ms total) 18: 18: [----------] 4 tests from ArrayRefFromBoolTypeVector 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.Works 18: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 18: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 18: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 18: 18: [----------] 7 tests from CStringUtilityTest 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 18: [ RUN ] CStringUtilityTest.strip_comment 18: [ OK ] CStringUtilityTest.strip_comment (0 ms) 18: [ RUN ] CStringUtilityTest.upstring 18: [ OK ] CStringUtilityTest.upstring (0 ms) 18: [ RUN ] CStringUtilityTest.ltrim 18: [ OK ] CStringUtilityTest.ltrim (0 ms) 18: [ RUN ] CStringUtilityTest.rtrim 18: [ OK ] CStringUtilityTest.rtrim (0 ms) 18: [ RUN ] CStringUtilityTest.trim 18: [ OK ] CStringUtilityTest.trim (0 ms) 18: [----------] 7 tests from CStringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from DefaultInitializationAllocator 18: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 18: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 18: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 18: 18: [----------] 4 tests from EnumerationHelpersTest 18: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 18: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 18: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 18: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 18: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 18: 18: [----------] 1 test from EnumClassSuitsEnumerationArray 18: [ RUN ] EnumClassSuitsEnumerationArray.Works 18: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 18: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 18: 18: [----------] 18 tests from FixedCapacityVectorTest 18: [ RUN ] FixedCapacityVectorTest.IsEmpty 18: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 18: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PushWorks 18: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PopWorks 18: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ResizeWorks 18: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ClearWorks 18: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 18: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.AtThrows 18: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 18: [ RUN ] FixedCapacityVectorTest.IteratorWorks 18: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 18: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 18: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 18: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 18: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.DataWorks 18: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 18: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 18: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 18: 18: [----------] 7 tests from TreeValueTransformTest 18: [ RUN ] TreeValueTransformTest.SimpleTransforms 18: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 18: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 18: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromString 18: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 18: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 18: [ RUN ] TreeValueTransformTest.ScopedTransformRules 18: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 18: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 18: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 18: [----------] 7 tests from TreeValueTransformTest (0 ms total) 18: 18: [----------] 1 test from TreeValueTransformErrorTest 18: [ RUN ] TreeValueTransformErrorTest.ConversionError 18: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 18: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 18: 18: [----------] 9 tests from ListOfLists 18: [ RUN ] ListOfLists.EmptyListOfListsWorks 18: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 18: [ RUN ] ListOfLists.AppendWorks 18: [ OK ] ListOfLists.AppendWorks (0 ms) 18: [ RUN ] ListOfLists.EmptyListWorks 18: [ OK ] ListOfLists.EmptyListWorks (0 ms) 18: [ RUN ] ListOfLists.AppendAccessWorks 18: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 18: [ RUN ] ListOfLists.ClearWorks 18: [ OK ] ListOfLists.ClearWorks (0 ms) 18: [ RUN ] ListOfLists.OutOfRangeAccessThrows 18: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 18: [ RUN ] ListOfLists.FrontAndBackWork 18: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 18: [ RUN ] ListOfLists.ExtractsAndRestores 18: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 18: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 18: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 18: [----------] 9 tests from ListOfLists (0 ms total) 18: 18: [----------] 7 tests from LoggerTest 18: [ RUN ] LoggerTest.EmptyLoggerWorks 18: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToStream 18: [ OK ] LoggerTest.LogsToStream (0 ms) 18: [ RUN ] LoggerTest.LogsToFile 18: [ OK ] LoggerTest.LogsToFile (0 ms) 18: [ RUN ] LoggerTest.LevelFilteringWorks 18: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleStreams 18: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleFiles 18: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 18: [ RUN ] LoggerTest.LogsToStreamAndFile 18: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 18: [----------] 7 tests from LoggerTest (0 ms total) 18: 18: [----------] 7 tests from MessageStringCollectorTest 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 18: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 18: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveAssign 18: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 18: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 18: 18: [----------] 12 tests from MpiComm 18: [ RUN ] MpiComm.SingleRankNoComm 18: [ OK ] MpiComm.SingleRankNoComm (0 ms) 18: [ RUN ] MpiComm.CommWorld 18: [ OK ] MpiComm.CommWorld (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: ./src/gromacs/utility/tests/mpicomm.cpp:160: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:168: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:181: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:194: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 18: [ RUN ] MpiComm.ConstructorThrowsOnNull 18: ./src/gromacs/utility/tests/mpicomm.cpp:206: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull (0 ms) 18: [ RUN ] MpiComm.CopyConstructorWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:220: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CopyConstructorWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:243: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:259: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:281: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:298: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 18: [----------] 12 tests from MpiComm (0 ms total) 18: 18: [----------] 1 test from PathTest 18: [ RUN ] PathTest.StripSourcePrefixWorks 18: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 18: [----------] 1 test from PathTest (0 ms total) 18: 18: [----------] 2 tests from PhysicalNodeCommunicatorTest 18: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 18: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 18: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 18: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 18: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 18: 18: [----------] 5 tests from Range 18: [ RUN ] Range.EmptyRangeWorks 18: [ OK ] Range.EmptyRangeWorks (0 ms) 18: [ RUN ] Range.NonEmptyRangeWorks 18: [ OK ] Range.NonEmptyRangeWorks (0 ms) 18: [ RUN ] Range.BeginEnd 18: [ OK ] Range.BeginEnd (0 ms) 18: [ RUN ] Range.IsInRangeWorks 18: [ OK ] Range.IsInRangeWorks (0 ms) 18: [ RUN ] Range.IteratorWorks 18: [ OK ] Range.IteratorWorks (0 ms) 18: [----------] 5 tests from Range (0 ms total) 18: 18: [----------] 3 tests from ScopeGuardTest 18: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 18: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 18: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 18: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 18: [----------] 3 tests from ScopeGuardTest (0 ms total) 18: 18: [----------] 7 tests from StringConvert 18: [ RUN ] StringConvert.NoResultFromEptyString 18: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 18: [ RUN ] StringConvert.ThreeFloatsSuccessfully 18: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 18: [ RUN ] StringConvert.OneIntSucessfully 18: [ OK ] StringConvert.OneIntSucessfully (0 ms) 18: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 18: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 18: [ RUN ] StringConvert.ThrowsWhenWrongSize 18: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 18: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 18: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 18: [----------] 7 tests from StringConvert (0 ms total) 18: 18: [----------] 7 tests from StringToEnumValueConverterTest 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 18: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 18: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 18: 18: [----------] 9 tests from StringUtilityTest 18: [ RUN ] StringUtilityTest.StartsWith 18: [ OK ] StringUtilityTest.StartsWith (0 ms) 18: [ RUN ] StringUtilityTest.EndsWith 18: [ OK ] StringUtilityTest.EndsWith (0 ms) 18: [ RUN ] StringUtilityTest.StripSuffixIfPresent 18: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 18: [ RUN ] StringUtilityTest.StripString 18: [ OK ] StringUtilityTest.StripString (0 ms) 18: [ RUN ] StringUtilityTest.SplitString 18: [ OK ] StringUtilityTest.SplitString (0 ms) 18: [ RUN ] StringUtilityTest.SplitDelimitedString 18: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 18: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 18: [----------] 9 tests from StringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from FormatStringTest 18: [ RUN ] FormatStringTest.HandlesBasicFormatting 18: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 18: [ RUN ] FormatStringTest.HandlesLongStrings 18: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 18: [----------] 2 tests from FormatStringTest (0 ms total) 18: 18: [----------] 1 test from StringFormatterTest 18: [ RUN ] StringFormatterTest.HandlesBasicFormatting 18: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 18: [----------] 1 test from StringFormatterTest (0 ms total) 18: 18: [----------] 1 test from formatAndJoinTest 18: [ RUN ] formatAndJoinTest.Works 18: [ OK ] formatAndJoinTest.Works (0 ms) 18: [----------] 1 test from formatAndJoinTest (0 ms total) 18: 18: [----------] 1 test from JoinStringsTest 18: [ RUN ] JoinStringsTest.Works 18: [ OK ] JoinStringsTest.Works (0 ms) 18: [----------] 1 test from JoinStringsTest (0 ms total) 18: 18: [----------] 6 tests from ReplaceAllTest 18: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 18: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesNoMatches 18: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 18: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 18: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 18: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 18: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 18: [----------] 6 tests from ReplaceAllTest (0 ms total) 18: 18: [----------] 10 tests from TextLineWrapperTest 18: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 18: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 18: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 18: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectly 18: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndent 18: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 18: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 18: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 18: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 18: [----------] 10 tests from TextLineWrapperTest (0 ms total) 18: 18: [----------] 1 test from PrettyPrintListAsRangeTest 18: [ RUN ] PrettyPrintListAsRangeTest.Works 18: [ OK ] PrettyPrintListAsRangeTest.Works (0 ms) 18: [----------] 1 test from PrettyPrintListAsRangeTest (0 ms total) 18: 18: [----------] 1 test from CompileTimeStringJoin 18: [ RUN ] CompileTimeStringJoin.Works 18: [ OK ] CompileTimeStringJoin.Works (0 ms) 18: [----------] 1 test from CompileTimeStringJoin (0 ms total) 18: 18: [----------] 3 tests from TemplateMPTest 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 18: [----------] 3 tests from TemplateMPTest (0 ms total) 18: 18: [----------] 8 tests from TextWriterTest 18: [ RUN ] TextWriterTest.WritesLines 18: [ OK ] TextWriterTest.WritesLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInParts 18: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 18: [ RUN ] TextWriterTest.WritesWrappedLines 18: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 18: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 18: [ RUN ] TextWriterTest.TracksNewlines 18: [ OK ] TextWriterTest.TracksNewlines (0 ms) 18: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 18: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 18: [ RUN ] TextWriterTest.WritesIndentedLines 18: [ OK ] TextWriterTest.WritesIndentedLines (0 ms) 18: [ RUN ] TextWriterTest.ScopedIndenterWritesIndentedLines 18: [ OK ] TextWriterTest.ScopedIndenterWritesIndentedLines (0 ms) 18: [----------] 8 tests from TextWriterTest (0 ms total) 18: 18: [----------] 4 tests from DumpingTextTest 18: [ RUN ] DumpingTextTest.LegacyIndentingWorks 18: [ OK ] DumpingTextTest.LegacyIndentingWorks (0 ms) 18: [ RUN ] DumpingTextTest.ReportsWhenNotAvailableIdentically 18: [ OK ] DumpingTextTest.ReportsWhenNotAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.QuietWhenAvailableIdentically 18: [ OK ] DumpingTextTest.QuietWhenAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.PrintsTitleAndSizeIdentically 18: [ OK ] DumpingTextTest.PrintsTitleAndSizeIdentically (0 ms) 18: [----------] 4 tests from DumpingTextTest (0 ms total) 18: 18: [----------] 1 test from TypeTraitsTest 18: [ RUN ] TypeTraitsTest.IsIntegralConstant 18: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 18: [----------] 1 test from TypeTraitsTest (0 ms total) 18: 18: [----------] 41 tests from RVecTest 18: [ RUN ] RVecTest.CanBeStoredInVector 18: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAsMutable_rvec 18: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Array 18: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 18: [ RUN ] RVecTest.ComparesEqual 18: [ OK ] RVecTest.ComparesEqual (0 ms) 18: [ RUN ] RVecTest.ComparesUnequal 18: [ OK ] RVecTest.ComparesUnequal (0 ms) 18: [ RUN ] RVecTest.CanAddRVecToRvec 18: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanAddAssignRVecToRvec 18: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractRVecFromRvec 18: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 18: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanDotProductRVecByRvec 18: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanCrossProductRVecByRvec 18: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVecInplace 18: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 18: [ RUN ] RVecTest.CanScaleRVec 18: [ OK ] RVecTest.CanScaleRVec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVec 18: [ OK ] RVecTest.CanDivideRVec (0 ms) 18: [ RUN ] RVecTest.CanDoUnitvFromRVec 18: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanSqLengthOfRVec 18: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanLengthOfRVec 18: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToRVec 18: [ OK ] RVecTest.CanCastToRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToDVec 18: [ OK ] RVecTest.CanCastToDVec (0 ms) 18: [ RUN ] RVecTest.CanLeftScalarMultiply 18: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanRightScalarMultiply 18: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanGetUnitvFromRVec 18: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanGetSqLengthOfRVec 18: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanGetLengthOfRVec 18: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoCrossProductOfRVec 18: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoDotProductOfRVec 18: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanScaleByVector 18: [ OK ] RVecTest.CanScaleByVector (0 ms) 18: [ RUN ] RVecTest.CanNegate 18: [ OK ] RVecTest.CanNegate (0 ms) 18: [ RUN ] RVecTest.asIVec 18: [ OK ] RVecTest.asIVec (0 ms) 18: [ RUN ] RVecTest.elementWiseMin 18: [ OK ] RVecTest.elementWiseMin (0 ms) 18: [ RUN ] RVecTest.elementWiseMax 18: [ OK ] RVecTest.elementWiseMax (0 ms) 18: [ RUN ] RVecTest.WorksAs_dvec_Reference 18: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_ivec_Reference 18: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Reference 18: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 18: [ RUN ] RVecTest.CopyConstructorWorks 18: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 18: [ RUN ] RVecTest.CopyAssignmentWorks 18: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.MoveConstructorWorks 18: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 18: [ RUN ] RVecTest.MoveAssignmentWorks 18: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.UsableInConstexpr 18: [ OK ] RVecTest.UsableInConstexpr (0 ms) 18: [----------] 41 tests from RVecTest (0 ms total) 18: 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 18: 18: [----------] 11 tests from WithInputPaths/PathSearchTest 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 18: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 18: 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 18: 18: [----------] 24 tests from Works/DumpingVectorsTest 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 (0 ms) 18: [----------] 24 tests from Works/DumpingVectorsTest (1 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 495 tests from 68 test suites ran. (8 ms total) 18: [ PASSED ] 485 tests. 18: [ SKIPPED ] 10 tests, listed below: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull 18: [ SKIPPED ] MpiComm.CopyConstructorWorks 18: [ SKIPPED ] MpiComm.AssigmentWorks 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf 18: 18: YOU HAVE 1 DISABLED TEST 18: 18/104 Test #18: UtilityUnitTests .......................... Passed 0.02 sec test 19 Start 19: MpiCommTests 19: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mpicomm-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MpiCommTests.xml" 19: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests 19: Test timeout computed to be: 30 19: [==========] Running 12 tests from 1 test suite. 19: [----------] Global test environment set-up. 19: [----------] 12 tests from MpiComm 19: [ RUN ] MpiComm.SingleRankNoComm 19: [ OK ] MpiComm.SingleRankNoComm (0 ms) 19: [ RUN ] MpiComm.CommWorld 19: [ OK ] MpiComm.CommWorld (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 19: [ RUN ] MpiComm.ConstructorThrowsOnNull 19: [ OK ] MpiComm.ConstructorThrowsOnNull (0 ms) 19: [ RUN ] MpiComm.CopyConstructorWorks 19: [ OK ] MpiComm.CopyConstructorWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorks 19: [ OK ] MpiComm.AssigmentWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorksForSelf 19: [ OK ] MpiComm.AssigmentWorksForSelf (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorks 19: [ OK ] MpiComm.MoveAssigmentWorks (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 19: [ OK ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 19: [----------] 12 tests from MpiComm (3 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 12 tests from 1 test suite ran. (3 ms total) 19: [ PASSED ] 12 tests. 19/104 Test #19: MpiCommTests .............................. Passed 0.02 sec test 20 Start 20: UtilityMpiUnitTests 20: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/utility/tests 20: Test timeout computed to be: 30 20: [==========] Running 7 tests from 2 test suites. 20: [----------] Global test environment set-up. 20: [----------] 5 tests from CoordinateExceptionHandlingTest 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow (0 ms) 20: [----------] 5 tests from CoordinateExceptionHandlingTest (1 ms total) 20: 20: [----------] 2 tests from PhysicalNodeCommunicatorTest 20: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 20: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 20: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 20: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 20: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 7 tests from 2 test suites ran. (1 ms total) 20: [ PASSED ] 7 tests. 20/104 Test #20: UtilityMpiUnitTests ....................... Passed 0.01 sec test 21 Start 21: MdlibUnitTest 21: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests 21: Test timeout computed to be: 30 21: [==========] Running 1042 tests from 29 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from EffectiveAtomDensity 21: [ RUN ] EffectiveAtomDensity.VolumeIndependence 21: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 21: [ RUN ] EffectiveAtomDensity.WeightingWorks 21: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 21: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 21: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 21: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 21: 21: [----------] 2 tests from AtomNonbondedAndKineticProperties 21: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 21: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 21: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 21: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 21: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 21: 21: [----------] 1 test from VerletBufferConstraintTest 21: [ RUN ] VerletBufferConstraintTest.EqualMasses 21: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 21: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 21: 21: [----------] 1 test from VerletBufferSize 21: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 21: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 21: [----------] 1 test from VerletBufferSize (0 ms total) 21: 21: [----------] 6 tests from CalcvirTest 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 21: [----------] 6 tests from CalcvirTest (0 ms total) 21: 21: [----------] 2 tests from PrEbinTest 21: [ RUN ] PrEbinTest.HandlesAverages 21: [ OK ] PrEbinTest.HandlesAverages (0 ms) 21: [ RUN ] PrEbinTest.HandlesEmptyAverages 21: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 21: [----------] 2 tests from PrEbinTest (0 ms total) 21: 21: [----------] 3 tests from EnergyDriftTracker 21: [ RUN ] EnergyDriftTracker.emptyWorks 21: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.onePointWorks 21: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.manyPointsWorks 21: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 21: [----------] 3 tests from EnergyDriftTracker (0 ms total) 21: 21: [----------] 4 tests from ShakeTest 21: [ RUN ] ShakeTest.ConstrainsOneBond 21: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 21: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 21: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 21: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 21: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 21: [----------] 4 tests from ShakeTest (0 ms total) 21: 21: [----------] 1 test from NullSignalTest 21: [ RUN ] NullSignalTest.NullSignallerWorks 21: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 21: [----------] 1 test from NullSignalTest (0 ms total) 21: 21: [----------] 7 tests from SignalTest 21: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 21: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 21: [----------] 7 tests from SignalTest (0 ms total) 21: 21: [----------] 13 tests from UpdateGroupsTest 21: [ RUN ] UpdateGroupsTest.WithEthaneUA 21: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 21: [ RUN ] UpdateGroupsTest.WithMethane 21: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithEthane 21: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 21: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 21: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFourSite 21: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 21: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 21: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 21: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 21: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 21: [----------] 13 tests from UpdateGroupsTest (0 ms total) 21: 21: [----------] 1 test from UpdateGroupsCog 21: [ RUN ] UpdateGroupsCog.ComputesCogs 21: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 21: [----------] 1 test from UpdateGroupsCog (0 ms total) 21: 21: [----------] 3 tests from VSiteTest 21: [ RUN ] VSiteTest.VSiteLowerConstructingWorks 21: [ OK ] VSiteTest.VSiteLowerConstructingWorks (0 ms) 21: [ RUN ] VSiteTest.VSiteHigherConstructingThrows 21: [ OK ] VSiteTest.VSiteHigherConstructingThrows (0 ms) 21: [ RUN ] VSiteTest.VSiteEqualConstructingThrows 21: [ OK ] VSiteTest.VSiteEqualConstructingThrows (0 ms) 21: [----------] 3 tests from VSiteTest (0 ms total) 21: 21: [----------] 2 tests from WholeMoleculeTransform 21: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 21: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 21: [ RUN ] WholeMoleculeTransform.HandlesReordering 21: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 21: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 21: 21: [----------] 28 tests from WithParameters/ConstraintsTest 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (4 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (3 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 21: [----------] 28 tests from WithParameters/ConstraintsTest (10 ms total) 21: 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 (1 ms) 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest (1 ms total) 21: 21: [----------] 11 tests from WithParameters/EnergyOutputTest 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 21: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 21: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 21: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 21: [----------] 11 tests from WithParameters/EnergyOutputTest (10 ms total) 21: 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 21: 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 21: 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 21: 21: [----------] 17 tests from WithParameters/LangevinTest 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 21: [----------] 17 tests from WithParameters/LangevinTest (1 ms total) 21: 21: [----------] 16 tests from WithParameters/LeapFrogTest 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 21: [----------] 16 tests from WithParameters/LeapFrogTest (8 ms total) 21: 21: [----------] 140 tests from Cubic/ParrRahmTest 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Cubic/ParrRahmTest (6 ms total) 21: 21: [----------] 140 tests from Rectilinear/ParrRahmTest 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Rectilinear/ParrRahmTest (7 ms total) 21: 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (8 ms total) 21: 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (8 ms total) 21: 21: [----------] 140 tests from TruncOct/ParrRahmTest 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from TruncOct/ParrRahmTest (11 ms total) 21: 21: [----------] 140 tests from Other/ParrRahmTest 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Other/ParrRahmTest (11 ms total) 21: 21: [----------] 13 tests from WithParameters/SettleTest 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 21: [----------] 13 tests from WithParameters/SettleTest (6 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1042 tests from 29 test suites ran. (98 ms total) 21: [ PASSED ] 1042 tests. 21/104 Test #21: MdlibUnitTest ............................. Passed 8.88 sec test 22 Start 22: AwhTest 22: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/AwhTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/awh/tests 22: Test timeout computed to be: 30 22: [==========] Running 27 tests from 10 test suites. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from SerializationTest 22: [ RUN ] SerializationTest.CanSerializeDimParams 22: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeBiasParams 22: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeAwhParams 22: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 22: [----------] 3 tests from SerializationTest (0 ms total) 22: 22: [----------] 1 test from BiasTest 22: [ RUN ] BiasTest.DetectsCovering 22: [ OK ] BiasTest.DetectsCovering (0 ms) 22: [----------] 1 test from BiasTest (0 ms total) 22: 22: [----------] 1 test from biasGridTest 22: [ RUN ] biasGridTest.neighborhood 22: [ OK ] biasGridTest.neighborhood (0 ms) 22: [----------] 1 test from biasGridTest (0 ms total) 22: 22: [----------] 2 tests from BiasSharingTest 22: [ RUN ] BiasSharingTest.SharingWorks 22: [ OK ] BiasSharingTest.SharingWorks (0 ms) 22: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 22: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (1 ms) 22: [----------] 2 tests from BiasSharingTest (2 ms total) 22: 22: [----------] 2 tests from BiasFepLambdaStateTest 22: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 22: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 22: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 22: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 22: [----------] 2 tests from BiasFepLambdaStateTest (1 ms total) 22: 22: [----------] 8 tests from WithParameters/BiasTest 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 22: [----------] 8 tests from WithParameters/BiasTest (2 ms total) 22: 22: [----------] 2 tests from WithParameters/BiasStateTest 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 22: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 22: 22: [----------] 1 test from WithParameters/UserInputTest 22: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 22: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 22: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 22: 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (4 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (15 ms total) 22: 22: [----------] 3 tests from WithParameters/FrictionMetricTest 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (11 ms) 22: [----------] 3 tests from WithParameters/FrictionMetricTest (12 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 27 tests from 10 test suites ran. (37 ms total) 22: [ PASSED ] 27 tests. 22/104 Test #22: AwhTest ................................... Passed 0.05 sec test 23 Start 23: DensityFittingAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 23: Test timeout computed to be: 30 23: [==========] Running 18 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from DensityFittingTest 23: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 23: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 23: [ RUN ] DensityFittingTest.SingleAtom 23: [ OK ] DensityFittingTest.SingleAtom (0 ms) 23: [----------] 2 tests from DensityFittingTest (1 ms total) 23: 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest 23: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 23: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 23: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 23: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 23: 23: [----------] 1 test from DensityFittingForceProviderState 23: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 23: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 23: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 23: 23: [----------] 8 tests from DensityFittingOptionsTest 23: [ RUN ] DensityFittingOptionsTest.DefaultParameters 23: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 23: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 23: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 23: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 23: [ RUN ] DensityFittingOptionsTest.KvtToInternal 23: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 23: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 23: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 23: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 18 tests from 4 test suites ran. (1 ms total) 23: [ PASSED ] 18 tests. 23/104 Test #23: DensityFittingAppliedForcesUnitTest ....... Passed 0.01 sec test 24 Start 24: QMMMAppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 24: Test timeout computed to be: 30 24: [==========] Running 28 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 2 tests from QMMMInputGeneratorTest 24: [ RUN ] QMMMInputGeneratorTest.CanConstruct 24: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 24: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 24: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 24: [----------] 2 tests from QMMMInputGeneratorTest (0 ms total) 24: 24: [----------] 6 tests from QMMMTopologyPreprocessorTest 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Setting the LD random seed to -1077968897 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (4 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Setting the LD random seed to 532478591 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (3 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading -0.41000 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -91265441 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (4 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 63.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 129.093 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -67184010 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (8 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: 24: NOTE 2 [file unknown]: 24: You are using constraints on all bonds, whereas the forcefield has been 24: parametrized only with constraints involving hydrogen atoms. We suggest 24: using constraints = h-bonds instead, this will also improve performance. 24: 24: 24: NOTE 3 [file unknown]: 24: For energy conservation with LINCS, lincs_iter should be 2 or larger. 24: 24: 24: Number of degrees of freedom in T-Coupling group rest is 42.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 193.640 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 5 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: 24: WARNING 2 [file unknown]: 24: Your embedded subsystem has a lot of constrained bonds. They probably 24: have been generated automatically. That could produce artifacts in the 24: simulation. Consider constraints = none in the mdp file. 24: 24: 24: Setting the LD random seed to -1277231777 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: turning all bonds into constraints... 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (9 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Number of degrees of freedom in T-Coupling group rest is 45.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 24: Setting the LD random seed to -629230087 24: 24: Generated 3 of the 6 non-bonded parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'VSTEST' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 24: 24: Cleaning up constraints and constant bonded interactions with virtual sites 24: Analysing residue names: 24: There are: 1 Other residues 24: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (3 ms) 24: [----------] 6 tests from QMMMTopologyPreprocessorTest (34 ms total) 24: 24: [----------] 9 tests from QMMMOptionsTest 24: [ RUN ] QMMMOptionsTest.DefaultParameters 24: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 24: [ RUN ] QMMMOptionsTest.OptionSetsActive 24: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 24: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 24: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 24: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 24: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 24: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 24: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 24: [----------] 9 tests from QMMMOptionsTest (1 ms total) 24: 24: [----------] 3 tests from QMMMForceProviderStateTest 24: [ RUN ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint 24: [ OK ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent 24: [ OK ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.MissingStateWhenNoData 24: [ OK ] QMMMForceProviderStateTest.MissingStateWhenNoData (0 ms) 24: [----------] 3 tests from QMMMForceProviderStateTest (0 ms total) 24: 24: [----------] 1 test from QMMMForceProviderTest 24: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 24: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 24: [----------] 1 test from QMMMForceProviderTest (0 ms total) 24: 24: [----------] 1 test from QMMMTest 24: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 24: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 24: [----------] 1 test from QMMMTest (0 ms total) 24: 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink (0 ms) 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 28 tests from 7 test suites ran. (36 ms total) 24: [ PASSED ] 28 tests. 24/104 Test #24: QMMMAppliedForcesUnitTest ................. Passed 0.05 sec test 25 Start 25: ColvarsAppliedForcesUnitTest 25: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests 25: Test timeout computed to be: 30 25: [==========] Running 16 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 1 test from ColvarsTest 25: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 25: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 25: [----------] 1 test from ColvarsTest (0 ms total) 25: 25: [----------] 6 tests from ColvarsOptionsTest 25: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 25: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OptionSetsActive 25: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to -33100 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (4 ms) 25: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 25: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 25: [----------] 6 tests from ColvarsOptionsTest (5 ms total) 25: 25: [----------] 4 tests from ColvarsPreProcessorTest 25: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to -8650857 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to -332137721 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to -1079009459 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (3 ms) 25: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to -1426216001 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (3 ms) 25: [----------] 4 tests from ColvarsPreProcessorTest (13 ms total) 25: 25: [----------] 5 tests from ColvarsForceProviderTest 25: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 25: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 25: [ RUN ] ColvarsForceProviderTest.SimpleInputs 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to -1278315137 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 25: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to 1740586843 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (2 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to 1337786367 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForces4water (3 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 66.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: NVE simulation: will use the initial temperature of 300.368 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 25: Setting the LD random seed to -301074033 25: 25: Generated 2211 of the 2211 non-bonded parameter combinations 25: 25: Generated 2211 of the 2211 1-4 parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 25: Analysing residue names: 25: There are: 2 Protein residues 25: Analysing Protein... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (10 ms) 25: [----------] 5 tests from ColvarsForceProviderTest (21 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 16 tests from 4 test suites ran. (39 ms total) 25: [ PASSED ] 16 tests. 25/104 Test #25: ColvarsAppliedForcesUnitTest .............. Passed 0.05 sec test 26 Start 26: PlumedAppliedForcesUnitTests 26: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests 26: Test timeout computed to be: 30 26: [==========] Running 8 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 8 tests from PlumedOptionsTest 26: [ RUN ] PlumedOptionsTest.defaultConstructor 26: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 26: [ RUN ] PlumedOptionsTest.setTimeStep 26: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 26: [ RUN ] PlumedOptionsTest.setStartingBehavior 26: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFile 26: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 26: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 26: [ RUN ] PlumedOptionsTest.setTopology 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 21.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: 26: NOTE 2 [file angles1.top, line 72]: 26: In moleculetype 'butane' 4 atoms are not bound by a potential or 26: constraint to any other atom in the same moleculetype. Although 26: technically this might not cause issues in a simulation, this often means 26: that the user forgot to add a bond/potential/constraint or put multiple 26: molecules in the same moleculetype definition by mistake. Run with -v to 26: get information for each atom. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: NVE simulation: will use the initial temperature of 238.919 K for 26: determining the Verlet buffer size 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 17493.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: NVE simulation: will use the initial temperature of 67.983 K for 26: determining the Verlet buffer size 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 18.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: NVE simulation: will use the initial temperature of 135.187 K for 26: determining the Verlet buffer size 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 26: Setting the LD random seed to 1436794443 26: 26: Generated 10 of the 10 non-bonded parameter combinations 26: 26: Generated 10 of the 10 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Water residues 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -1116742044 26: 26: Generated 3 of the 3 non-bonded parameter combinations 26: 26: Excluding 3 bonded neighbours molecule type 'butane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/angles1.gro' 26: Analysing residue names: 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to 1073739763 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Argon' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon5832.gro' 26: Analysing residue names: 26: There are: 5832 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to 1973420027 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonA' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonB' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonC' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonD' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -152307973 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Dipole' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 26: Analysing residue names: 26: There are: 2 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -1108011041 26: 26: Generated 331705 of the 331705 non-bonded parameter combinations 26: 26: Generated 331705 of the 331705 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Excluding 3 bonded neighbours molecule type 'methane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc_and_methane.gro' 26: Analysing residue names: 26: There are: 1 Water residues 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: [ OK ] PlumedOptionsTest.setTopology (323 ms) 26: [----------] 8 tests from PlumedOptionsTest (324 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 8 tests from 1 test suite ran. (324 ms total) 26: [ PASSED ] 8 tests. 26/104 Test #26: PlumedAppliedForcesUnitTests .............. Passed 0.34 sec test 27 Start 27: PlumedMDTests 27: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/PlumedMDTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests 27: Test timeout computed to be: 600 27: [==========] Running 2 tests from 1 test suite. 27: [----------] Global test environment set-up. 27: [----------] 2 tests from SimplePlumedMD/PlumedRun 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 27: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 2 tests from 1 test suite ran. (15 ms total) 27: [ PASSED ] 0 tests. 27: [ SKIPPED ] 2 tests, listed below: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27/104 Test #27: PlumedMDTests ............................. Passed 0.03 sec test 28 Start 28: NNPotAppliedForcesUnitTest 28: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 28: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests 28: Test timeout computed to be: 30 28: [==========] Running 17 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 1 test from NNPotTest 28: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 28: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 28: [----------] 1 test from NNPotTest (0 ms total) 28: 28: [----------] 5 tests from NNPotOptionsTest 28: [ RUN ] NNPotOptionsTest.DefaultParameters 28: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 28: [ RUN ] NNPotOptionsTest.OptionSetsActive 28: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 28: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 28: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 28: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 28: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 28: [----------] 5 tests from NNPotOptionsTest (0 ms total) 28: 28: [----------] 1 test from NNPotForceProviderTest 28: [ RUN ] NNPotForceProviderTest.CanConstruct 28: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 28: [----------] 1 test from NNPotForceProviderTest (0 ms total) 28: 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Setting the LD random seed to -69221647 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 (4 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Setting the LD random seed to -738732705 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Setting the LD random seed to 486111189 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 (438 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Setting the LD random seed to -609225729 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Setting the LD random seed to -425869841 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 (8 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: Setting the LD random seed to -268567591 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 (8 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: 28: WARNING 1 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -406851718 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 (8 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: 28: WARNING 2 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -537665541 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 (9 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Setting the LD random seed to -201330721 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 28: Setting the LD random seed to -574622245 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 (3 ms) 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest (491 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 17 tests from 4 test suites ran. (492 ms total) 28: [ PASSED ] 17 tests. 28/104 Test #28: NNPotAppliedForcesUnitTest ................ Passed 0.52 sec test 29 Start 29: AppliedForcesUnitTest 29: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 29: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/applied_forces/tests 29: Test timeout computed to be: 30 29: [==========] Running 3 tests from 1 test suite. 29: [----------] Global test environment set-up. 29: [----------] 3 tests from ElectricFieldTest 29: [ RUN ] ElectricFieldTest.Static 29: [ OK ] ElectricFieldTest.Static (0 ms) 29: [ RUN ] ElectricFieldTest.Oscillating 29: [ OK ] ElectricFieldTest.Oscillating (0 ms) 29: [ RUN ] ElectricFieldTest.Pulsed 29: [ OK ] ElectricFieldTest.Pulsed (0 ms) 29: [----------] 3 tests from ElectricFieldTest (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 3 tests from 1 test suite ran. (0 ms total) 29: [ PASSED ] 3 tests. 29/104 Test #29: AppliedForcesUnitTest ..................... Passed 0.01 sec test 30 Start 30: ListedForcesTest 30: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 30: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/listed_forces/tests 30: Test timeout computed to be: 30 30: [==========] Running 132 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from Bond/ListedForcesTest 30: [ RUN ] Bond/ListedForcesTest.Ifunc/0 30: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/1 30: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/2 30: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/3 30: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/4 30: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/5 30: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/6 30: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/7 30: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/8 30: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/9 30: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/10 30: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/11 30: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/12 30: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/13 30: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/14 30: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/15 30: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/16 30: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/17 30: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/18 30: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/19 30: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/20 30: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/21 30: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/22 30: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/23 30: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 30: [----------] 24 tests from Bond/ListedForcesTest (2 ms total) 30: 30: [----------] 33 tests from Angle/ListedForcesTest 30: [ RUN ] Angle/ListedForcesTest.Ifunc/0 30: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/1 30: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/2 30: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/3 30: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/4 30: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/5 30: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/6 30: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/7 30: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/8 30: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/9 30: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/10 30: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/11 30: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/12 30: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/13 30: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/14 30: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/15 30: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/16 30: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/17 30: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/18 30: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/19 30: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/20 30: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/21 30: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/22 30: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/23 30: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/24 30: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/25 30: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/26 30: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/27 30: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/28 30: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/29 30: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/30 30: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/31 30: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/32 30: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 30: [----------] 33 tests from Angle/ListedForcesTest (3 ms total) 30: 30: [----------] 18 tests from Dihedral/ListedForcesTest 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Dihedral/ListedForcesTest (2 ms total) 30: 30: [----------] 12 tests from Polarize/ListedForcesTest 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 30: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 30: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 30: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 30: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 30: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 30: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 30: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 30: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 30: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 30: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 30: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 30: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 30: 30: [----------] 18 tests from Restraints/ListedForcesTest 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 30: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 30: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 30: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 30: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 30: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 30: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 30: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 30: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 30: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 30: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 30: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 30: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 30: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 30: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 30: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 30: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 30: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 30: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Restraints/ListedForcesTest (2 ms total) 30: 30: [----------] 3 tests from BondZeroLength/ListedForcesTest 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 30: 30: [----------] 3 tests from AngleZero/ListedForcesTest 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 30: 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) 30: 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 132 tests from 9 test suites ran. (14 ms total) 30: [ PASSED ] 132 tests. 30/104 Test #30: ListedForcesTest .......................... Passed 0.03 sec test 31 Start 31: NbnxmTests 31: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nbnxm-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests 31: Test timeout computed to be: 30 31: [==========] Running 532 tests from 5 test suites. 31: [----------] Global test environment set-up. 31: [----------] 19 tests from KernelSetupTest 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 31: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 31: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeNone 31: [ OK ] KernelSetupTest.getCoulombKernelTypeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 31: [----------] 19 tests from KernelSetupTest (0 ms total) 31: 31: [----------] 2 tests from SimdEnergyAccumulatorTest 31: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 31: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 31: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 31: 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 31: 31: [----------] 504 tests from Combinations/NbnxmKernelTest 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [----------] 504 tests from Combinations/NbnxmKernelTest (415 ms total) 31: 31: [----------] 4 tests from WithParameters/PlainPairlistTest 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 (1 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:241: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 (0 ms) 31: [----------] 4 tests from WithParameters/PlainPairlistTest (2 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 532 tests from 5 test suites ran. (419 ms total) 31: [ PASSED ] 189 tests. 31: [ SKIPPED ] 343 tests, listed below: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31/104 Test #31: NbnxmTests ................................ Passed 0.44 sec test 32 Start 32: NbnxmGpuTests 32: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests 32: Test timeout computed to be: 30 32: This test program does NOT link in any test case. Please make sure this is intended. 32: [==========] Running 0 tests from 0 test suites. 32: [==========] 0 tests from 0 test suites ran. (0 ms total) 32: [ PASSED ] 0 tests. 32/104 Test #32: NbnxmGpuTests ............................. Passed 0.02 sec test 33 Start 33: GmxlibTests 33: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests 33: Test timeout computed to be: 30 33: [==========] Running 78 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 72 tests from NBInteraction/NonbondedFepTest 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 33: [----------] 72 tests from NBInteraction/NonbondedFepTest (6 ms total) 33: 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 78 tests from 2 test suites ran. (7 ms total) 33: [ PASSED ] 78 tests. 33/104 Test #33: GmxlibTests ............................... Passed 0.03 sec test 34 Start 34: GmxlibGpuTests 34: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/nonbonded-fep-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GmxlibGpuTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/nbnxm/tests 34: Test timeout computed to be: 30 34: This test program does NOT link in any test case. Please make sure this is intended. 34: [==========] Running 0 tests from 0 test suites. 34: [==========] 0 tests from 0 test suites ran. (0 ms total) 34: [ PASSED ] 0 tests. 34/104 Test #34: GmxlibGpuTests ............................ Passed 0.02 sec test 35 Start 35: CommandLineUnitTests 35: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests 35: Test timeout computed to be: 30 35: [==========] Running 60 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from CommandLineHelpModuleTest 35: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 35: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 35: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 35: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 35: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 35: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 35: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 35: 35: [----------] 7 tests from CommandLineHelpWriterTest 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 35: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 35: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 35: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 35: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 35: 35: [----------] 6 tests from CommandLineModuleManagerTest 35: [ RUN ] CommandLineModuleManagerTest.RunsModule 35: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 35: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 35: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 35: 35: [----------] 13 tests from CommandLineParserTest 35: [ RUN ] CommandLineParserTest.HandlesSingleValues 35: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 35: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 35: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesString 35: [ OK ] CommandLineParserTest.HandlesString (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 35: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 35: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 35: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 35: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 35: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 35: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 35: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 35: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 35: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 35: [----------] 13 tests from CommandLineParserTest (0 ms total) 35: 35: [----------] 6 tests from CommandLineProgramContextTest 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 35: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 35: 35: [----------] 3 tests from OutputNamesTest 35: [ RUN ] OutputNamesTest.CanBeSuffixed 35: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 35: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 35: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 35: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 35: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 35: [----------] 3 tests from OutputNamesTest (0 ms total) 35: 35: [----------] 22 tests from ParseCommonArgsTest 35: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 35: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 35: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 35: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 35: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 35: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 35: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 35: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 35: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 35: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 35: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 35: Value is /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 35: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (2 ms) 35: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 35: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 35: [----------] 22 tests from ParseCommonArgsTest (4 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 60 tests from 7 test suites ran. (6 ms total) 35: [ PASSED ] 60 tests. 35/104 Test #35: CommandLineUnitTests ...................... Passed 0.02 sec test 36 Start 36: DomDecTests 36: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/DomDecTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests 36: Test timeout computed to be: 30 36: [==========] Running 9 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 7 tests from HashedMap 36: [ RUN ] HashedMap.InsertsFinds 36: [ OK ] HashedMap.InsertsFinds (0 ms) 36: [ RUN ] HashedMap.NegativeKeysWork 36: [ OK ] HashedMap.NegativeKeysWork (0 ms) 36: [ RUN ] HashedMap.InsertsErases 36: [ OK ] HashedMap.InsertsErases (0 ms) 36: [ RUN ] HashedMap.InsertsOrAssigns 36: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 36: [ RUN ] HashedMap.Clears 36: [ OK ] HashedMap.Clears (0 ms) 36: [ RUN ] HashedMap.LinkedEntries 36: [ OK ] HashedMap.LinkedEntries (0 ms) 36: [ RUN ] HashedMap.ResizesTable 36: [ OK ] HashedMap.ResizesTable (0 ms) 36: [----------] 7 tests from HashedMap (0 ms total) 36: 36: [----------] 2 tests from LocalAtomSetManager 36: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 36: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 36: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 36: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 36: [----------] 2 tests from LocalAtomSetManager (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 9 tests from 2 test suites ran. (0 ms total) 36: [ PASSED ] 9 tests. 36/104 Test #36: DomDecTests ............................... Passed 0.01 sec test 37 Start 37: DomDecMpiTests 37: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/domdec/tests 37: Test timeout computed to be: 30 37: [==========] Running 8 tests from 1 test suite. 37: [----------] Global test environment set-up. 37: [----------] 8 tests from Works/HaloExchangeTest 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/0 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/0 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/1 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/1 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/2 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/2 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/3 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/3 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/3 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 (0 ms) 37: [----------] 8 tests from Works/HaloExchangeTest (2 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 8 tests from 1 test suite ran. (2 ms total) 37: [ PASSED ] 4 tests. 37: [ SKIPPED ] 4 tests, listed below: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 37/104 Test #37: DomDecMpiTests ............................ Passed 0.03 sec test 38 Start 38: EwaldUnitTests 38: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/ewald/tests 38: Test timeout computed to be: 30 38: [==========] Running 407 tests from 9 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from SeparatePmeRanksPermittedTest 38: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 38: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 38: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 38: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 38: 38: [----------] 108 tests from Pme_SplineAndSpreadTest 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [----------] 108 tests from Pme_SplineAndSpreadTest (81 ms total) 38: 38: [----------] 64 tests from Pme_SolveTest 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from Pme_SolveTest (11 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (3 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (6 ms total) 38: 38: [----------] 64 tests from PmeDiffEps_SolveTest 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from PmeDiffEps_SolveTest (10 ms total) 38: 38: [----------] 72 tests from Pme_GatherTest 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [----------] 72 tests from Pme_GatherTest (11 ms total) 38: 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (2 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (2 ms total) 38: 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (3 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (3 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (3 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (68 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 407 tests from 9 test suites ran. (198 ms total) 38: [ PASSED ] 311 tests. 38: [ SKIPPED ] 96 tests, listed below: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38/104 Test #38: EwaldUnitTests ............................ Passed 0.23 sec test 39 Start 39: FFTUnitTests 39: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fft/tests 39: Test timeout computed to be: 1920 39: [==========] Running 15 tests from 4 test suites. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from ManyFFTTest 39: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (4 ms) 39: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (10 ms) 39: [----------] 2 tests from ManyFFTTest (15 ms total) 39: 39: [----------] 1 test from FFTTest 39: [ RUN ] FFTTest.Real2DLength18_15Test 39: [ OK ] FFTTest.Real2DLength18_15Test (3 ms) 39: [----------] 1 test from FFTTest (3 ms total) 39: 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (1 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (6 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (8 ms) 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (21 ms total) 39: 39: [----------] 2 tests from Works/ParameterizedFFTTest3D 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 39: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 15 tests from 4 test suites ran. (41 ms total) 39: [ PASSED ] 15 tests. 39/104 Test #39: FFTUnitTests .............................. Passed 0.07 sec test 40 Start 40: FmmInterfaceUnitTests 40: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/fmm-interface-tests "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/FmmInterfaceUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fmm/tests 40: Test timeout computed to be: 30 40: [==========] Running 18 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 10 tests from FmmMdpOptionsTest 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues 40: [ OK ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive 40: [ OK ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive (0 ms) 40: [----------] 10 tests from FmmMdpOptionsTest (0 ms total) 40: 40: [----------] 4 tests from FmmMdpValidatorTest 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings 40: 40: ERROR 1 [file unknown]: 40: ExaFMM expansion order must be greater than 0. 40: 40: 40: ERROR 1 [file unknown]: 40: ExaFMM direct range must be 2 when using GROMACS as a direct provider. 40: 40: 40: ERROR 1 [file unknown]: 40: Adaptive tree cannot be used for FMM when GROMACS is the direct provider. 40: Use a uniform tree instead. 40: 40: 40: ERROR 1 [file unknown]: 40: Maximum particles per cell for FMM must be set to a positive value when 40: using an adaptive tree. 40: 40: 40: ERROR 1 [file unknown]: 40: Tree depth for FMM is determined based on the domain decomposition grid 40: when using GROMACS as the direct provider and should not be set by the 40: user. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings 40: 40: ERROR 1 [file unknown]: 40: FMSolvr tree depth must be greater than or equal to 0. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings 40: [ OK ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm 40: 40: ERROR 1 [file unknown]: 40: FMM requires Coulomb interaction type to be FMM, but got PME 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm (0 ms) 40: [----------] 4 tests from FmmMdpValidatorTest (0 ms total) 40: 40: [----------] 1 test from FmmForceProviderTest 40: [ RUN ] FmmForceProviderTest.ThrowsWhenConstructingStub 40: [ OK ] FmmForceProviderTest.ThrowsWhenConstructingStub (0 ms) 40: [----------] 1 test from FmmForceProviderTest (0 ms total) 40: 40: [----------] 3 tests from FmmForceProviderBuilderTest 40: [ RUN ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady 40: [ OK ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup 40: [ OK ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider 40: [ OK ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider (0 ms) 40: [----------] 3 tests from FmmForceProviderBuilderTest (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 18 tests from 4 test suites ran. (1 ms total) 40: [ PASSED ] 18 tests. 40/104 Test #40: FmmInterfaceUnitTests ..................... Passed 0.01 sec test 41 Start 41: GpuUtilsUnitTests 41: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests 41: Test timeout computed to be: 30 41: [==========] Running 67 tests from 22 test suites. 41: [----------] Global test environment set-up. 41: [----------] 2 tests from ClfftInitializer 41: [ RUN ] ClfftInitializer.SingleInitializationWorks 41: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 41: [ RUN ] ClfftInitializer.TwoInitializationsWork 41: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 41: [----------] 2 tests from ClfftInitializer (0 ms total) 41: 41: [----------] 1 test from DevicesAvailable 41: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 41: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 41: [----------] 1 test from DevicesAvailable (0 ms total) 41: 41: [----------] 1 test from DeviceStreamManagerTest 41: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 41: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 41: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 41: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 41: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 41: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 41: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Swap 41: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Comparison 41: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 41: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 41: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Swap 41: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Comparison 41: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 41: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Swap 41: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Comparison 41: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 41: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Swap 41: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Comparison 41: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 41: 41: [----------] 1 test from HostAllocatorUntypedTest 41: [ RUN ] HostAllocatorUntypedTest.Comparison 41: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 41: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.Move 41: [ OK ] AllocatorTest/0.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/0 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.Move 41: [ OK ] AllocatorTest/1.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/1 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator,gmx::HostAllocationPolicy> 41: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.Move 41: [ OK ] AllocatorTest/2.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/2 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.Move 41: [ OK ] AllocatorTest/3.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/3 (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 67 tests from 22 test suites ran. (1 ms total) 41: [ PASSED ] 67 tests. 41/104 Test #41: GpuUtilsUnitTests ......................... Passed 0.02 sec test 42 Start 42: GpuUtilsMpiTests 42: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/gpu_utils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GpuUtilsMpiTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gpu_utils/tests 42: Test timeout computed to be: 30 42: [==========] Running 15 tests from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message (0 ms) 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/0_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/1_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/12000_values_in_message 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message (0 ms) 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest (2 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 15 tests from 1 test suite ran. (2 ms total) 42: [ PASSED ] 0 tests. 42: [ SKIPPED ] 15 tests, listed below: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: 42: YOU HAVE 3 DISABLED TESTS 42: 42/104 Test #42: GpuUtilsMpiTests .......................... Passed 0.03 sec test 43 Start 43: HardwareUnitTests 43: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/hardware/tests 43: Test timeout computed to be: 30 43: [==========] Running 22 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 1 test from CpuInfoTest 43: [ RUN ] CpuInfoTest.SupportLevel 43: [ OK ] CpuInfoTest.SupportLevel (1 ms) 43: [----------] 1 test from CpuInfoTest (1 ms total) 43: 43: [----------] 4 tests from HardwareTopologyTest 43: [ RUN ] HardwareTopologyTest.Execute 43: [ OK ] HardwareTopologyTest.Execute (13 ms) 43: [ RUN ] HardwareTopologyTest.HwlocExecute 43: [ OK ] HardwareTopologyTest.HwlocExecute (11 ms) 43: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 43: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (10 ms) 43: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 43: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (10 ms) 43: [----------] 4 tests from HardwareTopologyTest (45 ms total) 43: 43: [----------] 1 test from DevicesManagerTest 43: [ RUN ] DevicesManagerTest.Serialization 43: [ OK ] DevicesManagerTest.Serialization (0 ms) 43: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 43: [----------] 1 test from DevicesManagerTest (0 ms total) 43: 43: [----------] 1 test from UuidStringTest 43: [ RUN ] UuidStringTest.Works 43: [ OK ] UuidStringTest.Works (0 ms) 43: [----------] 1 test from UuidStringTest (0 ms total) 43: 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (2 ms total) 43: 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) 43: 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (0 ms total) 43: 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (0 ms total) 43: 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 43: 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 43: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 22 tests from 10 test suites ran. (56 ms total) 43: [ PASSED ] 22 tests. 43: 43: YOU HAVE 1 DISABLED TEST 43: 43/104 Test #43: HardwareUnitTests ......................... Passed 0.07 sec test 44 Start 44: MathUnitTests 44: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/math/tests 44: Test timeout computed to be: 30 44: [==========] Running 293 tests from 40 test suites. 44: [----------] Global test environment set-up. 44: [----------] 1 test from EmptyArrayRefWithPaddingTest 44: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 44: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 44: 44: [----------] 2 tests from InvertBoxMatrixTest 44: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 44: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 44: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 44: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 44: 44: [----------] 8 tests from ComplexNumberTest 44: [ RUN ] ComplexNumberTest.RealComplexMultiply 44: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 44: [ RUN ] ComplexNumberTest.RealComplexExp 44: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAdd 44: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexSubtract 44: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexMultiply 44: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexDivision 44: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexConjugate 44: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAbs2 44: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 44: [----------] 8 tests from ComplexNumberTest (0 ms total) 44: 44: [----------] 11 tests from TranslateAndScaleTest 44: [ RUN ] TranslateAndScaleTest.identityTransformation 44: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 44: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 44: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingIdentity 44: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 44: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 44: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 44: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 44: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 44: 44: [----------] 3 tests from AffineTransformationTest 44: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 44: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 44: [ RUN ] AffineTransformationTest.applyTransformationToVectors 44: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 44: [ RUN ] AffineTransformationTest.retrieveGradient 44: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 44: [----------] 3 tests from AffineTransformationTest (0 ms total) 44: 44: [----------] 14 tests from DensitySimilarityTest 44: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 44: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (18 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (16 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationCorrect 44: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 44: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 44: [----------] 14 tests from DensitySimilarityTest (37 ms total) 44: 44: [----------] 6 tests from StructureSimilarityTest 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 44: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 44: [----------] 6 tests from StructureSimilarityTest (0 ms total) 44: 44: [----------] 8 tests from ExponentialMovingAverage 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 44: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 44: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 44: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 44: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 44: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 44: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 44: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 44: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 44: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 44: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 44: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 44: 44: [----------] 21 tests from FunctionTest 44: [ RUN ] FunctionTest.StaticLog2 44: [ OK ] FunctionTest.StaticLog2 (0 ms) 44: [ RUN ] FunctionTest.Log2I32Bit 44: [ OK ] FunctionTest.Log2I32Bit (0 ms) 44: [ RUN ] FunctionTest.Log2I64Bit 44: [ OK ] FunctionTest.Log2I64Bit (0 ms) 44: [ RUN ] FunctionTest.GreatestCommonDivisor 44: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 44: [ RUN ] FunctionTest.InvsqrtFloat 44: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvsqrtDouble 44: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvsqrtInteger 44: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 44: [ RUN ] FunctionTest.InvcbrtFloat 44: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvcbrtDouble 44: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvcbrtInteger 44: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 44: [ RUN ] FunctionTest.SixthrootFloat 44: [ OK ] FunctionTest.SixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.SixthrootDouble 44: [ OK ] FunctionTest.SixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.SixthrootInteger 44: [ OK ] FunctionTest.SixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootFloat 44: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootDouble 44: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootInteger 44: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.Powers 44: [ OK ] FunctionTest.Powers (0 ms) 44: [ RUN ] FunctionTest.ErfInvFloat 44: [ OK ] FunctionTest.ErfInvFloat (0 ms) 44: [ RUN ] FunctionTest.ErfInvDouble 44: [ OK ] FunctionTest.ErfInvDouble (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 44: [----------] 21 tests from FunctionTest (1 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 44: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 44: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 44: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 44: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 44: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 44: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 44: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 44: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 44: 44: [----------] 4 tests from GaussianOn1DLattice 44: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 44: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 44: [ RUN ] GaussianOn1DLattice.isCorrect 44: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 44: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 44: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 44: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 44: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 44: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 44: 44: [----------] 9 tests from GaussTransformTest 44: [ RUN ] GaussTransformTest.isZeroUponConstruction 44: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 44: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 44: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 44: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 44: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 44: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 44: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 44: [ RUN ] GaussTransformTest.view 44: [ OK ] GaussTransformTest.view (0 ms) 44: [----------] 9 tests from GaussTransformTest (0 ms total) 44: 44: [----------] 3 tests from DensityFittingForce 44: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 44: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 44: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 44: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 44: [ RUN ] DensityFittingForce.pullsTowardsDerivative 44: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 44: [----------] 3 tests from DensityFittingForce (0 ms total) 44: 44: [----------] 2 tests from InvertMatrixTest 44: [ RUN ] InvertMatrixTest.IdentityIsImpotent 44: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertMatrixTest.ComputesInverse 44: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 44: [----------] 2 tests from InvertMatrixTest (0 ms total) 44: 44: [----------] 28 tests from MatrixTest 44: [ RUN ] MatrixTest.canSetFromArray 44: [ OK ] MatrixTest.canSetFromArray (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallyFromList 44: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallySingleValue 44: [ OK ] MatrixTest.canSetStaticallySingleValue (0 ms) 44: [ RUN ] MatrixTest.canConstructAndFill 44: [ OK ] MatrixTest.canConstructAndFill (0 ms) 44: [ RUN ] MatrixTest.canSetValues 44: [ OK ] MatrixTest.canSetValues (0 ms) 44: [ RUN ] MatrixTest.canCopyAssign 44: [ OK ] MatrixTest.canCopyAssign (0 ms) 44: [ RUN ] MatrixTest.canSwap 44: [ OK ] MatrixTest.canSwap (0 ms) 44: [ RUN ] MatrixTest.staticMultiDimArrayExtent 44: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MatrixTest.canAddMatrix 44: [ OK ] MatrixTest.canAddMatrix (0 ms) 44: [ RUN ] MatrixTest.canAddAssignMatrix 44: [ OK ] MatrixTest.canAddAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractMatrix 44: [ OK ] MatrixTest.canSubtractMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractAssignMatrix 44: [ OK ] MatrixTest.canSubtractAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canNegateMatrix 44: [ OK ] MatrixTest.canNegateMatrix (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarMultiplication 44: [ OK ] MatrixTest.MatrixScalarMultiplication (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarDivision 44: [ OK ] MatrixTest.MatrixScalarDivision (0 ms) 44: [ RUN ] MatrixTest.MatrixVectorMultiplicationOperator 44: [ OK ] MatrixTest.MatrixVectorMultiplicationOperator (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 44: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixMultiplication 44: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 44: [ RUN ] MatrixTest.determinantWorks 44: [ OK ] MatrixTest.determinantWorks (0 ms) 44: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 44: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 44: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 44: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 44: [ RUN ] MatrixTest.traceWorks 44: [ OK ] MatrixTest.traceWorks (0 ms) 44: [ RUN ] MatrixTest.transposeWorks 44: [ OK ] MatrixTest.transposeWorks (0 ms) 44: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 44: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 44: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 44: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.canFillLegacyMatrix 44: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.IdentityMatrix 44: [ OK ] MatrixTest.IdentityMatrix (0 ms) 44: [ RUN ] MatrixTest.DiagonalMatrix 44: [ OK ] MatrixTest.DiagonalMatrix (0 ms) 44: [----------] 28 tests from MatrixTest (0 ms total) 44: 44: [----------] 25 tests from MultiDimArrayTest 44: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 44: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 44: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 44: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 44: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 44: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 44: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 44: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 44: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 44: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 44: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 44: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 44: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapStatic 44: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapDynamic 44: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToView 44: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToConstView 44: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 44: [ RUN ] MultiDimArrayTest.viewBegin 44: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.viewEnd 44: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstBegin 44: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstEnd 44: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 44: [----------] 25 tests from MultiDimArrayTest (0 ms total) 44: 44: [----------] 4 tests from MultiDimArrayToMdSpanTest 44: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 44: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 44: 44: [----------] 9 tests from NelderMeadSimplexTest 44: [ RUN ] NelderMeadSimplexTest.BestVertex 44: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.WorstVertex 44: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 44: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 44: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 44: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 44: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 44: [ RUN ] NelderMeadSimplexTest.OrientedLength 44: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 44: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 44: 44: [----------] 2 tests from NelderMead 44: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 44: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 44: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 44: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 44: [----------] 2 tests from NelderMead (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ResizeWorks 44: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorks 44: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanCopyAssign 44: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanMoveAssign 44: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanSwap 44: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ResizeWorks 44: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorks 44: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanCopyAssign 44: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanMoveAssign 44: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanSwap 44: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ResizeWorks 44: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorks 44: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanCopyAssign 44: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanMoveAssign 44: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanSwap 44: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ResizeWorks 44: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorks 44: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanCopyAssign 44: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanMoveAssign 44: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanSwap 44: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ResizeWorks 44: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorks 44: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanCopyAssign 44: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanMoveAssign 44: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanSwap 44: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ResizeWorks 44: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorks 44: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanCopyAssign 44: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanMoveAssign 44: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanSwap 44: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ResizeWorks 44: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorks 44: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanCopyAssign 44: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanMoveAssign 44: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanSwap 44: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ResizeWorks 44: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorks 44: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanCopyAssign 44: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanMoveAssign 44: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanSwap 44: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ResizeWorks 44: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorks 44: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanCopyAssign 44: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanMoveAssign 44: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanSwap 44: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ResizeWorks 44: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorks 44: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanCopyAssign 44: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanMoveAssign 44: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanSwap 44: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 293 tests from 40 test suites ran. (43 ms total) 44: [ PASSED ] 293 tests. 44/104 Test #44: MathUnitTests ............................. Passed 0.06 sec test 45 Start 45: MdrunUtilityUnitTests 45: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests 45: Test timeout computed to be: 30 45: [==========] Running 33 tests from 3 test suites. 45: [----------] Global test environment set-up. 45: [----------] 4 tests from MDModulesNotifierTest 45: [ RUN ] MDModulesNotifierTest.AddConsumer 45: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 45: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 45: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 45: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 45: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 45: 45: [----------] 1 test from PlainPairlistRanges 45: [ RUN ] PlainPairlistRanges.RmsdDistance 45: [ OK ] PlainPairlistRanges.RmsdDistance (0 ms) 45: [----------] 1 test from PlainPairlistRanges (0 ms total) 45: 45: [----------] 28 tests from ThreadAffinityTest 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 45: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 45: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 45: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 45: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndFullMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndFullMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask (0 ms) 45: [ RUN ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall 45: [ OK ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithSmt (1 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToECoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem (0 ms) 45: [----------] 28 tests from ThreadAffinityTest (7 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 33 tests from 3 test suites ran. (7 ms total) 45: [ PASSED ] 33 tests. 45/104 Test #45: MdrunUtilityUnitTests ..................... Passed 0.02 sec test 46 Start 46: MdrunUtilityMpiUnitTests 46: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdrunutility/tests 46: Test timeout computed to be: 30 46: [==========] Running 17 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 10 tests from ThreadAffinityMultiRankTest 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 46: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (1 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (1 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 46: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 46: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp (4 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken (1 ms) 46: [----------] 10 tests from ThreadAffinityMultiRankTest (11 ms total) 46: 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (2 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (6 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 17 tests from 2 test suites ran. (18 ms total) 46: [ PASSED ] 17 tests. 46/104 Test #46: MdrunUtilityMpiUnitTests .................. Passed 0.03 sec test 47 Start 47: MDSpanTests 47: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdspan/tests 47: Test timeout computed to be: 30 47: [==========] Running 32 tests from 7 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from BasicAccessorPolicy 47: [ RUN ] BasicAccessorPolicy.Decay 47: [ OK ] BasicAccessorPolicy.Decay (0 ms) 47: [ RUN ] BasicAccessorPolicy.Access 47: [ OK ] BasicAccessorPolicy.Access (0 ms) 47: [ RUN ] BasicAccessorPolicy.Offset 47: [ OK ] BasicAccessorPolicy.Offset (0 ms) 47: [ RUN ] BasicAccessorPolicy.CopyAccessor 47: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 47: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 47: 47: [----------] 4 tests from ExtentsTest 47: [ RUN ] ExtentsTest.Construction 47: [ OK ] ExtentsTest.Construction (0 ms) 47: [ RUN ] ExtentsTest.PurelyStatic 47: [ OK ] ExtentsTest.PurelyStatic (0 ms) 47: [ RUN ] ExtentsTest.RankNought 47: [ OK ] ExtentsTest.RankNought (0 ms) 47: [ RUN ] ExtentsTest.Assignment 47: [ OK ] ExtentsTest.Assignment (0 ms) 47: [----------] 4 tests from ExtentsTest (0 ms total) 47: 47: [----------] 8 tests from MdSpanExtension 47: [ RUN ] MdSpanExtension.SlicingAllStatic 47: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingDynamic 47: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingAllStatic3D 47: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 47: [ RUN ] MdSpanExtension.SlicingEqualsView3D 47: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 47: [ RUN ] MdSpanExtension.additionWorks 47: [ OK ] MdSpanExtension.additionWorks (0 ms) 47: [ RUN ] MdSpanExtension.subtractionWorks 47: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 47: [ RUN ] MdSpanExtension.multiplicationWorks 47: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 47: [ RUN ] MdSpanExtension.divisionWorks 47: [ OK ] MdSpanExtension.divisionWorks (0 ms) 47: [----------] 8 tests from MdSpanExtension (0 ms total) 47: 47: [----------] 3 tests from LayoutTests 47: [ RUN ] LayoutTests.LayoutRightConstruction 47: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 47: [ RUN ] LayoutTests.LayoutRightProperties 47: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 47: [ RUN ] LayoutTests.LayoutRightOperator 47: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 47: [----------] 3 tests from LayoutTests (0 ms total) 47: 47: [----------] 1 test from MdSpanTest 47: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 47: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 47: [----------] 1 test from MdSpanTest (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/0.Rank 47: [ OK ] MdSpanTest/0.Rank (0 ms) 47: [ RUN ] MdSpanTest/0.DynamicRank 47: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/0.Extents 47: [ OK ] MdSpanTest/0.Extents (0 ms) 47: [ RUN ] MdSpanTest/0.Strides 47: [ OK ] MdSpanTest/0.Strides (0 ms) 47: [ RUN ] MdSpanTest/0.Properties 47: [ OK ] MdSpanTest/0.Properties (0 ms) 47: [ RUN ] MdSpanTest/0.Operator 47: [ OK ] MdSpanTest/0.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/0 (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/1.Rank 47: [ OK ] MdSpanTest/1.Rank (0 ms) 47: [ RUN ] MdSpanTest/1.DynamicRank 47: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/1.Extents 47: [ OK ] MdSpanTest/1.Extents (0 ms) 47: [ RUN ] MdSpanTest/1.Strides 47: [ OK ] MdSpanTest/1.Strides (0 ms) 47: [ RUN ] MdSpanTest/1.Properties 47: [ OK ] MdSpanTest/1.Properties (0 ms) 47: [ RUN ] MdSpanTest/1.Operator 47: [ OK ] MdSpanTest/1.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/1 (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 32 tests from 7 test suites ran. (0 ms total) 47: [ PASSED ] 32 tests. 47/104 Test #47: MDSpanTests ............................... Passed 0.01 sec test 48 Start 48: MdtypesUnitTest 48: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/mdtypes/tests 48: Test timeout computed to be: 30 48: [==========] Running 98 tests from 7 test suites. 48: [----------] Global test environment set-up. 48: [----------] 4 tests from ForeingLambdaTermsDhdl 48: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 48: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 48: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 48: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 48: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 48: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 48: 48: [----------] 4 tests from ObservablesReducerTest 48: [ RUN ] ObservablesReducerTest.CanMoveAssign 48: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 48: [ RUN ] ObservablesReducerTest.CanMoveConstruct 48: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 48: [----------] 4 tests from ObservablesReducerTest (0 ms total) 48: 48: [----------] 3 tests from CheckpointDataTest 48: [ RUN ] CheckpointDataTest.SingleDataTest 48: [ OK ] CheckpointDataTest.SingleDataTest (5 ms) 48: [ RUN ] CheckpointDataTest.MultiDataTest 48: [ OK ] CheckpointDataTest.MultiDataTest (11 ms) 48: [ RUN ] CheckpointDataTest.EmptyVectorTest 48: [ OK ] CheckpointDataTest.EmptyVectorTest (0 ms) 48: [----------] 3 tests from CheckpointDataTest (16 ms total) 48: 48: [----------] 7 tests from ForceBuffers 48: [ RUN ] ForceBuffers.ConstructsUnpinned 48: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsPinned 48: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsEmpty 48: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 48: [ RUN ] ForceBuffers.ResizeWorks 48: [ OK ] ForceBuffers.ResizeWorks (0 ms) 48: [ RUN ] ForceBuffers.PaddingWorks 48: [ OK ] ForceBuffers.PaddingWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyWorks 48: [ OK ] ForceBuffers.CopyWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyDoesNotPin 48: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 48: [----------] 7 tests from ForceBuffers (0 ms total) 48: 48: [----------] 5 tests from MultipleTimeStepping 48: [ RUN ] MultipleTimeStepping.ChecksNumLevels 48: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 48: [ RUN ] MultipleTimeStepping.SelectsForceGroups 48: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksStepFactor 48: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 48: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksIntegrator 48: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 48: [----------] 5 tests from MultipleTimeStepping (0 ms total) 48: 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 48: 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 98 tests from 7 test suites ran. (17 ms total) 48: [ PASSED ] 98 tests. 48/104 Test #48: MdtypesUnitTest ........................... Passed 0.03 sec test 49 Start 49: OnlineHelpUnitTests 49: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/onlinehelp/tests 49: Test timeout computed to be: 30 49: [==========] Running 22 tests from 4 test suites. 49: [----------] Global test environment set-up. 49: [----------] 6 tests from TextTableFormatterTest 49: [ RUN ] TextTableFormatterTest.HandlesBasicCase 49: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesIndentation 49: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 49: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 49: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 49: [----------] 6 tests from TextTableFormatterTest (0 ms total) 49: 49: [----------] 3 tests from HelpManagerTest 49: [ RUN ] HelpManagerTest.HandlesRootTopic 49: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 49: [ RUN ] HelpManagerTest.HandlesSubTopics 49: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 49: [ RUN ] HelpManagerTest.HandlesInvalidTopics 49: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 49: [----------] 3 tests from HelpManagerTest (0 ms total) 49: 49: [----------] 2 tests from HelpTopicFormattingTest 49: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 49: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 49: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 49: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 49: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 49: 49: [----------] 11 tests from HelpWriterContextTest 49: [ RUN ] HelpWriterContextTest.FormatsParagraphs 49: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 49: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 49: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralText 49: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsBulletList 49: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 49: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 49: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsGridTable 49: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsTitles 49: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 49: [----------] 11 tests from HelpWriterContextTest (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 22 tests from 4 test suites ran. (1 ms total) 49: [ PASSED ] 22 tests. 49/104 Test #49: OnlineHelpUnitTests ....................... Passed 0.01 sec test 50 Start 50: OptionsUnitTests 50: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/options/tests 50: Test timeout computed to be: 30 50: [==========] Running 151 tests from 21 test suites. 50: [----------] Global test environment set-up. 50: [----------] 5 tests from AbstractOptionStorageTest 50: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 50: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 50: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 50: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 50: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 50: 50: [----------] 10 tests from FileNameOptionTest 50: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 50: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 50: [----------] 10 tests from FileNameOptionTest (0 ms total) 50: 50: [----------] 16 tests from FileNameOptionManagerTest 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 50: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 50: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 50: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 50: 50: [----------] 1 test from OptionsTest 50: [ RUN ] OptionsTest.FailsOnNonsafeStorage 50: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 50: [----------] 1 test from OptionsTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerTest 50: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 50: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 50: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMissingValue 50: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesExtraValue 50: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesGroups 50: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesSections 50: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 50: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 50: [----------] 9 tests from OptionsAssignerTest (0 ms total) 50: 50: [----------] 4 tests from OptionsAssignerBooleanTest 50: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 50: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 50: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 50: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 50: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 50: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerIntegerTest 50: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerInt64Test 50: [ RUN ] OptionsAssignerInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresToVector 50: [ OK ] OptionsAssignerInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerInt64Test (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresToVector 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test (0 ms total) 50: 50: [----------] 5 tests from OptionsAssignerDoubleTest 50: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 50: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 50: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 50: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerStringTest 50: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 50: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 50: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 50: 50: [----------] 6 tests from OptionsAssignerEnumTest 50: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 50: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 50: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 50: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 50: 50: [----------] 8 tests from RepeatingOptionSectionTest 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 50: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 50: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 50: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 50: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 50: 50: [----------] 1 test from TimeUnitManagerTest 50: [ RUN ] TimeUnitManagerTest.BasicOperations 50: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 50: [----------] 1 test from TimeUnitManagerTest (0 ms total) 50: 50: [----------] 4 tests from TimeUnitBehaviorTest 50: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 50: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 50: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 50: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 50: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 50: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 50: 50: [----------] 2 tests from TreeValueSupportAssignTest 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 50: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 50: 50: [----------] 1 test from TreeValueSupportAssignErrorTest 50: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 50: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 50: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 50: 50: [----------] 5 tests from TreeValueSupportCheckTest 50: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 50: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 50: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 50: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 50: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 50: 50: [----------] 6 tests from TreeValueSupportAdjustTest 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 50: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 50: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 50: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 50: 50: [----------] 7 tests from TreeValueSupportTest 50: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 50: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 50: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsInt64Option 50: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsStringOption 50: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsFloatOption 50: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 50: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsEnumOption 50: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 50: [----------] 7 tests from TreeValueSupportTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 151 tests from 21 test suites ran. (3 ms total) 50: [ PASSED ] 151 tests. 50/104 Test #50: OptionsUnitTests .......................... Passed 0.02 sec test 51 Start 51: PbcutilUnitTest 51: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 51: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pbcutil/tests 51: Test timeout computed to be: 30 51: [==========] Running 37 tests from 5 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ShiftTest 51: [ RUN ] ShiftTest.CoordinateShiftWorks 51: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 51: [----------] 1 test from ShiftTest (0 ms total) 51: 51: [----------] 2 tests from MShift 51: [ RUN ] MShift.shiftsAndUnshifts 51: [ OK ] MShift.shiftsAndUnshifts (0 ms) 51: [ RUN ] MShift.shiftsAndUnshiftsSelf 51: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 51: [----------] 2 tests from MShift (0 ms total) 51: 51: [----------] 5 tests from PbcTest 51: [ RUN ] PbcTest.CalcShiftsWorks 51: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 51: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 51: [----------] 5 tests from PbcTest (0 ms total) 51: 51: [----------] 2 tests from PbcEnumsTest 51: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 51: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 51: [----------] 2 tests from PbcEnumsTest (0 ms total) 51: 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (3 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 37 tests from 5 test suites ran. (3 ms total) 51: [ PASSED ] 37 tests. 51/104 Test #51: PbcutilUnitTest ........................... Passed 0.01 sec test 52 Start 52: RandomUnitTests 52: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/random/tests 52: Test timeout computed to be: 30 52: [==========] Running 44 tests from 10 test suites. 52: [----------] Global test environment set-up. 52: [----------] 4 tests from ExponentialDistributionTest 52: [ RUN ] ExponentialDistributionTest.Output 52: [ OK ] ExponentialDistributionTest.Output (0 ms) 52: [ RUN ] ExponentialDistributionTest.Logical 52: [ OK ] ExponentialDistributionTest.Logical (0 ms) 52: [ RUN ] ExponentialDistributionTest.Reset 52: [ OK ] ExponentialDistributionTest.Reset (0 ms) 52: [ RUN ] ExponentialDistributionTest.AltParam 52: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 52: 52: [----------] 4 tests from GammaDistributionTest 52: [ RUN ] GammaDistributionTest.Output 52: [ OK ] GammaDistributionTest.Output (0 ms) 52: [ RUN ] GammaDistributionTest.Logical 52: [ OK ] GammaDistributionTest.Logical (0 ms) 52: [ RUN ] GammaDistributionTest.Reset 52: [ OK ] GammaDistributionTest.Reset (0 ms) 52: [ RUN ] GammaDistributionTest.AltParam 52: [ OK ] GammaDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from GammaDistributionTest (0 ms total) 52: 52: [----------] 4 tests from NormalDistributionTest 52: [ RUN ] NormalDistributionTest.Output 52: [ OK ] NormalDistributionTest.Output (0 ms) 52: [ RUN ] NormalDistributionTest.Logical 52: [ OK ] NormalDistributionTest.Logical (0 ms) 52: [ RUN ] NormalDistributionTest.Reset 52: [ OK ] NormalDistributionTest.Reset (0 ms) 52: [ RUN ] NormalDistributionTest.AltParam 52: [ OK ] NormalDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from NormalDistributionTest (0 ms total) 52: 52: [----------] 1 test from SeedTest 52: [ RUN ] SeedTest.makeRandomSeed 52: [ OK ] SeedTest.makeRandomSeed (0 ms) 52: [----------] 1 test from SeedTest (0 ms total) 52: 52: [----------] 6 tests from TabulatedNormalDistributionTest 52: [ RUN ] TabulatedNormalDistributionTest.Output14 52: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Output16 52: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 52: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Logical 52: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Reset 52: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.AltParam 52: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 52: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 52: 52: [----------] 1 test from TabulatedNormalDistributionTableTest 52: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 52: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 52: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 52: 52: [----------] 6 tests from ThreeFry2x64Test 52: [ RUN ] ThreeFry2x64Test.Logical 52: [ OK ] ThreeFry2x64Test.Logical (0 ms) 52: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 52: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 52: [ RUN ] ThreeFry2x64Test.Reseed 52: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 52: [ RUN ] ThreeFry2x64Test.Discard 52: [ OK ] ThreeFry2x64Test.Discard (0 ms) 52: [ RUN ] ThreeFry2x64Test.InvalidCounter 52: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 52: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 52: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 52: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 52: 52: [----------] 4 tests from UniformIntDistributionTest 52: [ RUN ] UniformIntDistributionTest.Output 52: [ OK ] UniformIntDistributionTest.Output (0 ms) 52: [ RUN ] UniformIntDistributionTest.Logical 52: [ OK ] UniformIntDistributionTest.Logical (0 ms) 52: [ RUN ] UniformIntDistributionTest.Reset 52: [ OK ] UniformIntDistributionTest.Reset (0 ms) 52: [ RUN ] UniformIntDistributionTest.AltParam 52: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 52: 52: [----------] 5 tests from UniformRealDistributionTest 52: [ RUN ] UniformRealDistributionTest.GenerateCanonical 52: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Output 52: [ OK ] UniformRealDistributionTest.Output (0 ms) 52: [ RUN ] UniformRealDistributionTest.Logical 52: [ OK ] UniformRealDistributionTest.Logical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Reset 52: [ OK ] UniformRealDistributionTest.Reset (0 ms) 52: [ RUN ] UniformRealDistributionTest.AltParam 52: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 52: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 52: 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 44 tests from 10 test suites ran. (2 ms total) 52: [ PASSED ] 44 tests. 52/104 Test #52: RandomUnitTests ........................... Passed 0.02 sec test 53 Start 53: RestraintTests 53: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/RestraintTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/restraint/tests 53: Test timeout computed to be: 30 53: [==========] Running 1 test from 1 test suite. 53: [----------] Global test environment set-up. 53: [----------] 1 test from RestraintManager 53: [ RUN ] RestraintManager.restraintList 53: [ OK ] RestraintManager.restraintList (0 ms) 53: [----------] 1 test from RestraintManager (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 1 test from 1 test suite ran. (0 ms total) 53: [ PASSED ] 1 test. 53/104 Test #53: RestraintTests ............................ Passed 0.01 sec test 54 Start 54: SerializationUnitTests 54: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/serialization-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/SerializationUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/serialization/tests 54: Test timeout computed to be: 30 54: [==========] Running 9 tests from 2 test suites. 54: [----------] Global test environment set-up. 54: [----------] 5 tests from InMemorySerializerTest 54: [ RUN ] InMemorySerializerTest.Roundtrip 54: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 54: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 54: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SizeIsCorrect 54: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 54: [----------] 5 tests from InMemorySerializerTest (0 ms total) 54: 54: [----------] 4 tests from KeyValueTreeSerializerTest 54: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 54: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 54: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 54: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 9 tests from 2 test suites ran. (0 ms total) 54: [ PASSED ] 9 tests. 54/104 Test #54: SerializationUnitTests .................... Passed 0.01 sec test 55 Start 55: TableUnitTests 55: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tables/tests 55: Test timeout computed to be: 30 55: [==========] Running 20 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 55: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/0.Sinc 55: [ OK ] SplineTableTest/0.Sinc (0 ms) 55: [ RUN ] SplineTableTest/0.LJ12 55: [ OK ] SplineTableTest/0.LJ12 (8 ms) 55: [ RUN ] SplineTableTest/0.PmeCorrection 55: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/0.TwoFunctions 55: [ OK ] SplineTableTest/0.TwoFunctions (13 ms) 55: [ RUN ] SplineTableTest/0.ThreeFunctions 55: [ OK ] SplineTableTest/0.ThreeFunctions (12 ms) 55: [ RUN ] SplineTableTest/0.Simd 55: [ OK ] SplineTableTest/0.Simd (2 ms) 55: [ RUN ] SplineTableTest/0.SimdTwoFunctions 55: [ OK ] SplineTableTest/0.SimdTwoFunctions (11 ms) 55: [----------] 10 tests from SplineTableTest/0 (50 ms total) 55: 55: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 55: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/1.Sinc 55: [ OK ] SplineTableTest/1.Sinc (0 ms) 55: [ RUN ] SplineTableTest/1.LJ12 55: [ OK ] SplineTableTest/1.LJ12 (17 ms) 55: [ RUN ] SplineTableTest/1.PmeCorrection 55: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/1.TwoFunctions 55: [ OK ] SplineTableTest/1.TwoFunctions (33 ms) 55: [ RUN ] SplineTableTest/1.ThreeFunctions 55: [ OK ] SplineTableTest/1.ThreeFunctions (35 ms) 55: [ RUN ] SplineTableTest/1.Simd 55: [ OK ] SplineTableTest/1.Simd (5 ms) 55: [ RUN ] SplineTableTest/1.SimdTwoFunctions 55: [ OK ] SplineTableTest/1.SimdTwoFunctions (27 ms) 55: [----------] 10 tests from SplineTableTest/1 (122 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 20 tests from 2 test suites ran. (172 ms total) 55: [ PASSED ] 20 tests. 55/104 Test #55: TableUnitTests ............................ Passed 0.18 sec test 56 Start 56: TaskAssignmentUnitTests 56: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/taskassignment/tests 56: Test timeout computed to be: 30 56: [==========] Running 3 tests from 2 test suites. 56: [----------] Global test environment set-up. 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 56: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 56: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 56: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 56: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 56: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 56: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 3 tests from 2 test suites ran. (0 ms total) 56: [ PASSED ] 3 tests. 56/104 Test #56: TaskAssignmentUnitTests ................... Passed 0.01 sec test 57 Start 57: GmxTimingTests 57: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/timing/tests 57: Test timeout computed to be: 30 57: [==========] Running 6 tests from 1 test suite. 57: [----------] Global test environment set-up. 57: [----------] 6 tests from TimingTest 57: [ RUN ] TimingTest.ElementCountingWorks 57: [ OK ] TimingTest.ElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.ElementNoCountingWorks 57: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementCountingWorks 57: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementNoCountingWorks 57: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.RunWallCycle 57: [ OK ] TimingTest.RunWallCycle (1 ms) 57: [ RUN ] TimingTest.RunWallCycleSub 57: [ OK ] TimingTest.RunWallCycleSub (0 ms) 57: [----------] 6 tests from TimingTest (1 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 6 tests from 1 test suite ran. (1 ms total) 57: [ PASSED ] 6 tests. 57/104 Test #57: GmxTimingTests ............................ Passed 0.01 sec test 58 Start 58: TopologyTest 58: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/TopologyTest.xml" 58: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/topology/tests 58: Test timeout computed to be: 30 58: [==========] Running 153 tests from 10 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from PdbAtomEntryTest 58: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 58: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 58: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 58: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 58: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 58: 58: [----------] 3 tests from ExclusionBlockTest 58: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 58: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 58: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 58: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 58: [ RUN ] ExclusionBlockTest.MergeExclusions 58: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 58: [----------] 3 tests from ExclusionBlockTest (0 ms total) 58: 58: [----------] 6 tests from InteractionListTest 58: [ RUN ] InteractionListTest.EmptyWorks 58: [ OK ] InteractionListTest.EmptyWorks (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArray 58: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 58: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionPointer 58: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 58: [ RUN ] InteractionListTest.CanAddListToOtherList 58: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 58: [ RUN ] InteractionListTest.ClearingWorks 58: [ OK ] InteractionListTest.ClearingWorks (0 ms) 58: [----------] 6 tests from InteractionListTest (0 ms total) 58: 58: [----------] 3 tests from IndexTest 58: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 58: [ RUN ] IndexTest.WriteIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteIndexWorks (1 ms) 58: [ RUN ] IndexTest.WriteAndReadIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 58: [----------] 3 tests from IndexTest (6 ms total) 58: 58: [----------] 4 tests from MtopTest 58: [ RUN ] MtopTest.RangeBasedLoop 58: [ OK ] MtopTest.RangeBasedLoop (0 ms) 58: [ RUN ] MtopTest.Operators 58: [ OK ] MtopTest.Operators (0 ms) 58: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 58: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 58: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 58: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 58: [----------] 4 tests from MtopTest (0 ms total) 58: 58: [----------] 2 tests from IListRangeTest 58: [ RUN ] IListRangeTest.RangeBasedLoopWorks 58: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 58: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 58: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 58: [----------] 2 tests from IListRangeTest (0 ms total) 58: 58: [----------] 13 tests from StringTableTest 58: [ RUN ] StringTableTest.AddSingleEntry 58: [ OK ] StringTableTest.AddSingleEntry (0 ms) 58: [ RUN ] StringTableTest.CanAccessWithAt 58: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 58: [ RUN ] StringTableTest.CanAccessWithBracket 58: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 58: [ RUN ] StringTableTest.ThrowsOutOfRange 58: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 58: [ RUN ] StringTableTest.StringCompareIsCorrect 58: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 58: [ RUN ] StringTableTest.AddTwoDistinctEntries 58: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] StringTableTest.TryToAddDuplicates 58: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 58: [ RUN ] StringTableTest.AddLargeNumberOfEntries 58: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 58: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 58: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 58: [ RUN ] StringTableTest.CanWriteToBuffer 58: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 58: [ RUN ] StringTableTest.Roundtrip 58: [ OK ] StringTableTest.Roundtrip (0 ms) 58: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 58: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 58: [ RUN ] StringTableTest.CanCopyToLegacyTable 58: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 58: [----------] 13 tests from StringTableTest (1 ms total) 58: 58: [----------] 6 tests from LegacySymtabTest 58: [ RUN ] LegacySymtabTest.EmptyOnOpen 58: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 58: [ RUN ] LegacySymtabTest.AddSingleEntry 58: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 58: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 58: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] LegacySymtabTest.TryToAddDuplicates 58: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 58: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 58: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 58: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 58: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 58: [----------] 6 tests from LegacySymtabTest (0 ms total) 58: 58: [----------] 5 tests from TopSortTest 58: [ RUN ] TopSortTest.WorksOnEmptyIdef 58: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 58: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 58: [----------] 5 tests from TopSortTest (0 ms total) 58: 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (7 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 153 tests from 10 test suites ran. (15 ms total) 58: [ PASSED ] 153 tests. 58: 58: YOU HAVE 1 DISABLED TEST 58: 58/104 Test #58: TopologyTest .............................. Passed 0.03 sec test 59 Start 59: PullTest 59: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/PullTest.xml" 59: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/pulling/tests 59: Test timeout computed to be: 30 59: [==========] Running 10 tests from 1 test suite. 59: [----------] Global test environment set-up. 59: [----------] 10 tests from PullTest 59: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 59: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 59: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 59: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 59: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 59: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 59: [ RUN ] PullTest.TransformationCoordSimple 59: [ OK ] PullTest.TransformationCoordSimple (0 ms) 59: [ RUN ] PullTest.TransformationCoordAdvanced 59: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 59: [ RUN ] PullTest.TransformationCoordTime 59: [ OK ] PullTest.TransformationCoordTime (0 ms) 59: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 59: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 59: [ RUN ] PullTest.TransformationCoordDummyExpression 59: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 59: [----------] 10 tests from PullTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 10 tests from 1 test suite ran. (0 ms total) 59: [ PASSED ] 10 tests. 59/104 Test #59: PullTest .................................. Passed 0.02 sec test 60 Start 60: SimdUnitTests 60: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/simd/tests 60: Test timeout computed to be: 30 60: [==========] Running 247 tests from 19 test suites. 60: [----------] Global test environment set-up. 60: [----------] 6 tests from SimdBootstrapTest 60: [ RUN ] SimdBootstrapTest.loadStore 60: [ OK ] SimdBootstrapTest.loadStore (0 ms) 60: [ RUN ] SimdBootstrapTest.loadU 60: [ OK ] SimdBootstrapTest.loadU (0 ms) 60: [ RUN ] SimdBootstrapTest.storeU 60: [ OK ] SimdBootstrapTest.storeU (0 ms) 60: [ RUN ] SimdBootstrapTest.loadStoreI 60: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 60: [ RUN ] SimdBootstrapTest.loadUI 60: [ OK ] SimdBootstrapTest.loadUI (0 ms) 60: [ RUN ] SimdBootstrapTest.storeUI 60: [ OK ] SimdBootstrapTest.storeUI (0 ms) 60: [----------] 6 tests from SimdBootstrapTest (0 ms total) 60: 60: [----------] 41 tests from SimdScalarTest 60: [ RUN ] SimdScalarTest.load 60: [ OK ] SimdScalarTest.load (0 ms) 60: [ RUN ] SimdScalarTest.loadU 60: [ OK ] SimdScalarTest.loadU (0 ms) 60: [ RUN ] SimdScalarTest.store 60: [ OK ] SimdScalarTest.store (0 ms) 60: [ RUN ] SimdScalarTest.storeU 60: [ OK ] SimdScalarTest.storeU (0 ms) 60: [ RUN ] SimdScalarTest.setZero 60: [ OK ] SimdScalarTest.setZero (0 ms) 60: [ RUN ] SimdScalarTest.andNot 60: [ OK ] SimdScalarTest.andNot (0 ms) 60: [ RUN ] SimdScalarTest.fma 60: [ OK ] SimdScalarTest.fma (0 ms) 60: [ RUN ] SimdScalarTest.fms 60: [ OK ] SimdScalarTest.fms (0 ms) 60: [ RUN ] SimdScalarTest.fnma 60: [ OK ] SimdScalarTest.fnma (0 ms) 60: [ RUN ] SimdScalarTest.fnms 60: [ OK ] SimdScalarTest.fnms (0 ms) 60: [ RUN ] SimdScalarTest.maskAdd 60: [ OK ] SimdScalarTest.maskAdd (0 ms) 60: [ RUN ] SimdScalarTest.maskzMul 60: [ OK ] SimdScalarTest.maskzMul (0 ms) 60: [ RUN ] SimdScalarTest.maskzFma 60: [ OK ] SimdScalarTest.maskzFma (0 ms) 60: [ RUN ] SimdScalarTest.abs 60: [ OK ] SimdScalarTest.abs (0 ms) 60: [ RUN ] SimdScalarTest.max 60: [ OK ] SimdScalarTest.max (0 ms) 60: [ RUN ] SimdScalarTest.min 60: [ OK ] SimdScalarTest.min (0 ms) 60: [ RUN ] SimdScalarTest.round 60: [ OK ] SimdScalarTest.round (0 ms) 60: [ RUN ] SimdScalarTest.trunc 60: [ OK ] SimdScalarTest.trunc (0 ms) 60: [ RUN ] SimdScalarTest.reduce 60: [ OK ] SimdScalarTest.reduce (0 ms) 60: [ RUN ] SimdScalarTest.testBits 60: [ OK ] SimdScalarTest.testBits (0 ms) 60: [ RUN ] SimdScalarTest.anyTrue 60: [ OK ] SimdScalarTest.anyTrue (0 ms) 60: [ RUN ] SimdScalarTest.selectByMask 60: [ OK ] SimdScalarTest.selectByMask (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMask 60: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 60: [ RUN ] SimdScalarTest.blend 60: [ OK ] SimdScalarTest.blend (0 ms) 60: [ RUN ] SimdScalarTest.cvtR2I 60: [ OK ] SimdScalarTest.cvtR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvttR2I 60: [ OK ] SimdScalarTest.cvttR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvtI2R 60: [ OK ] SimdScalarTest.cvtI2R (0 ms) 60: [ RUN ] SimdScalarTest.cvtF2D 60: [ OK ] SimdScalarTest.cvtF2D (0 ms) 60: [ RUN ] SimdScalarTest.cvtD2D 60: [ OK ] SimdScalarTest.cvtD2D (0 ms) 60: [ RUN ] SimdScalarTest.loadI 60: [ OK ] SimdScalarTest.loadI (0 ms) 60: [ RUN ] SimdScalarTest.loadUI 60: [ OK ] SimdScalarTest.loadUI (0 ms) 60: [ RUN ] SimdScalarTest.storeI 60: [ OK ] SimdScalarTest.storeI (0 ms) 60: [ RUN ] SimdScalarTest.storeUI 60: [ OK ] SimdScalarTest.storeUI (0 ms) 60: [ RUN ] SimdScalarTest.andNotI 60: [ OK ] SimdScalarTest.andNotI (0 ms) 60: [ RUN ] SimdScalarTest.testBitsI 60: [ OK ] SimdScalarTest.testBitsI (0 ms) 60: [ RUN ] SimdScalarTest.selectByMaskI 60: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMaskI 60: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 60: [ RUN ] SimdScalarTest.blendI 60: [ OK ] SimdScalarTest.blendI (0 ms) 60: [ RUN ] SimdScalarTest.cvtB2IB 60: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 60: [ RUN ] SimdScalarTest.cvtIB2B 60: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 60: [ RUN ] SimdScalarTest.expandScalarsToTriplets 60: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 60: [----------] 41 tests from SimdScalarTest (0 ms total) 60: 60: [----------] 8 tests from SimdScalarUtilTest 60: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 60: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 60: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 60: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 60: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 60: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 60: 60: [----------] 37 tests from SimdScalarMathTest 60: [ RUN ] SimdScalarMathTest.copysign 60: [ OK ] SimdScalarMathTest.copysign (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPair 60: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 60: [ RUN ] SimdScalarMathTest.inv 60: [ OK ] SimdScalarMathTest.inv (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrt 60: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdScalarMathTest.log 60: [ OK ] SimdScalarMathTest.log (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2 60: [ OK ] SimdScalarMathTest.exp2 (0 ms) 60: [ RUN ] SimdScalarMathTest.exp 60: [ OK ] SimdScalarMathTest.exp (0 ms) 60: [ RUN ] SimdScalarMathTest.erf 60: [ OK ] SimdScalarMathTest.erf (0 ms) 60: [ RUN ] SimdScalarMathTest.erfc 60: [ OK ] SimdScalarMathTest.erfc (0 ms) 60: [ RUN ] SimdScalarMathTest.sincos 60: [ OK ] SimdScalarMathTest.sincos (0 ms) 60: [ RUN ] SimdScalarMathTest.sin 60: [ OK ] SimdScalarMathTest.sin (0 ms) 60: [ RUN ] SimdScalarMathTest.cos 60: [ OK ] SimdScalarMathTest.cos (0 ms) 60: [ RUN ] SimdScalarMathTest.tan 60: [ OK ] SimdScalarMathTest.tan (0 ms) 60: [ RUN ] SimdScalarMathTest.asin 60: [ OK ] SimdScalarMathTest.asin (0 ms) 60: [ RUN ] SimdScalarMathTest.acos 60: [ OK ] SimdScalarMathTest.acos (0 ms) 60: [ RUN ] SimdScalarMathTest.atan 60: [ OK ] SimdScalarMathTest.atan (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2 60: [ OK ] SimdScalarMathTest.atan2 (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrection 60: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 60: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.invSingleAccuracy 60: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 60: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.logSingleAccuracy 60: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 60: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.expSingleAccuracy 60: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 60: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 60: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 60: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 60: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 60: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 60: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 60: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 60: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 37 tests from SimdScalarMathTest (0 ms total) 60: 60: [----------] 1 test from SimdTest 60: [ RUN ] SimdTest.GmxAligned 60: [ OK ] SimdTest.GmxAligned (0 ms) 60: [----------] 1 test from SimdTest (0 ms total) 60: 60: [----------] 42 tests from SimdFloatingpointTest 60: [ RUN ] SimdFloatingpointTest.setZero 60: [ OK ] SimdFloatingpointTest.setZero (0 ms) 60: [ RUN ] SimdFloatingpointTest.set 60: [ OK ] SimdFloatingpointTest.set (0 ms) 60: [ RUN ] SimdFloatingpointTest.add 60: [ OK ] SimdFloatingpointTest.add (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskAdd 60: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 60: [ RUN ] SimdFloatingpointTest.sub 60: [ OK ] SimdFloatingpointTest.sub (0 ms) 60: [ RUN ] SimdFloatingpointTest.mul 60: [ OK ] SimdFloatingpointTest.mul (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzMul 60: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 60: [ RUN ] SimdFloatingpointTest.fma 60: [ OK ] SimdFloatingpointTest.fma (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzFma 60: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fms 60: [ OK ] SimdFloatingpointTest.fms (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnma 60: [ OK ] SimdFloatingpointTest.fnma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnms 60: [ OK ] SimdFloatingpointTest.fnms (0 ms) 60: [ RUN ] SimdFloatingpointTest.abs 60: [ OK ] SimdFloatingpointTest.abs (0 ms) 60: [ RUN ] SimdFloatingpointTest.neg 60: [ OK ] SimdFloatingpointTest.neg (0 ms) 60: [ RUN ] SimdFloatingpointTest.and 60: [ OK ] SimdFloatingpointTest.and (0 ms) 60: [ RUN ] SimdFloatingpointTest.or 60: [ OK ] SimdFloatingpointTest.or (0 ms) 60: [ RUN ] SimdFloatingpointTest.xor 60: [ OK ] SimdFloatingpointTest.xor (0 ms) 60: [ RUN ] SimdFloatingpointTest.andNot 60: [ OK ] SimdFloatingpointTest.andNot (0 ms) 60: [ RUN ] SimdFloatingpointTest.max 60: [ OK ] SimdFloatingpointTest.max (0 ms) 60: [ RUN ] SimdFloatingpointTest.min 60: [ OK ] SimdFloatingpointTest.min (0 ms) 60: [ RUN ] SimdFloatingpointTest.round 60: [ OK ] SimdFloatingpointTest.round (0 ms) 60: [ RUN ] SimdFloatingpointTest.roundMode 60: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 60: [ RUN ] SimdFloatingpointTest.trunc 60: [ OK ] SimdFloatingpointTest.trunc (0 ms) 60: [ RUN ] SimdFloatingpointTest.frexp 60: [ OK ] SimdFloatingpointTest.frexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.ldexp 60: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.rsqrt 60: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRsqrt 60: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.rcp 60: [ OK ] SimdFloatingpointTest.rcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRcp 60: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 60: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.selectByNotMask 60: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpNe 60: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLe 60: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLt 60: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 60: [ RUN ] SimdFloatingpointTest.testBits 60: [ OK ] SimdFloatingpointTest.testBits (0 ms) 60: [ RUN ] SimdFloatingpointTest.andB 60: [ OK ] SimdFloatingpointTest.andB (0 ms) 60: [ RUN ] SimdFloatingpointTest.orB 60: [ OK ] SimdFloatingpointTest.orB (0 ms) 60: [ RUN ] SimdFloatingpointTest.anyTrueB 60: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 60: [ RUN ] SimdFloatingpointTest.blend 60: [ OK ] SimdFloatingpointTest.blend (0 ms) 60: [ RUN ] SimdFloatingpointTest.reduce 60: [ OK ] SimdFloatingpointTest.reduce (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 60: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 60: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 60: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 60: 60: [----------] 13 tests from SimdFloatingpointUtilTest 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 60: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 60: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 60: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 60: 60: [----------] 23 tests from SimdIntegerTest 60: [ RUN ] SimdIntegerTest.setZero 60: [ OK ] SimdIntegerTest.setZero (0 ms) 60: [ RUN ] SimdIntegerTest.set 60: [ OK ] SimdIntegerTest.set (0 ms) 60: [ RUN ] SimdIntegerTest.add 60: [ OK ] SimdIntegerTest.add (0 ms) 60: [ RUN ] SimdIntegerTest.sub 60: [ OK ] SimdIntegerTest.sub (0 ms) 60: [ RUN ] SimdIntegerTest.mul 60: [ OK ] SimdIntegerTest.mul (0 ms) 60: [ RUN ] SimdIntegerTest.and 60: [ OK ] SimdIntegerTest.and (0 ms) 60: [ RUN ] SimdIntegerTest.andNot 60: [ OK ] SimdIntegerTest.andNot (0 ms) 60: [ RUN ] SimdIntegerTest.or 60: [ OK ] SimdIntegerTest.or (0 ms) 60: [ RUN ] SimdIntegerTest.xor 60: [ OK ] SimdIntegerTest.xor (0 ms) 60: [ RUN ] SimdIntegerTest.extract 60: [ OK ] SimdIntegerTest.extract (0 ms) 60: [ RUN ] SimdIntegerTest.cvtR2I 60: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvttR2I 60: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvtI2R 60: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpLt 60: [ OK ] SimdIntegerTest.cmpLt (0 ms) 60: [ RUN ] SimdIntegerTest.testBits 60: [ OK ] SimdIntegerTest.testBits (0 ms) 60: [ RUN ] SimdIntegerTest.andB 60: [ OK ] SimdIntegerTest.andB (0 ms) 60: [ RUN ] SimdIntegerTest.orB 60: [ OK ] SimdIntegerTest.orB (0 ms) 60: [ RUN ] SimdIntegerTest.anyTrue 60: [ OK ] SimdIntegerTest.anyTrue (0 ms) 60: [ RUN ] SimdIntegerTest.blend 60: [ OK ] SimdIntegerTest.blend (0 ms) 60: [ RUN ] SimdIntegerTest.cvtB2IB 60: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 60: [ RUN ] SimdIntegerTest.cvtIB2B 60: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 60: [----------] 23 tests from SimdIntegerTest (0 ms total) 60: 60: [----------] 56 tests from SimdMathTest 60: [ RUN ] SimdMathTest.generateTestPointsDouble 60: [ OK ] SimdMathTest.generateTestPointsDouble (0 ms) 60: [ RUN ] SimdMathTest.copysign 60: [ OK ] SimdMathTest.copysign (0 ms) 60: [ RUN ] SimdMathTest.invsqrt 60: [ OK ] SimdMathTest.invsqrt (0 ms) 60: [ RUN ] SimdMathTest.maskzInvsqrt 60: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPair 60: [ OK ] SimdMathTest.invsqrtPair (0 ms) 60: [ RUN ] SimdMathTest.sqrt 60: [ OK ] SimdMathTest.sqrt (0 ms) 60: [ RUN ] SimdMathTest.sqrtUnsafe 60: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 60: [ RUN ] SimdMathTest.inv 60: [ OK ] SimdMathTest.inv (1 ms) 60: [ RUN ] SimdMathTest.maskzInv 60: [ OK ] SimdMathTest.maskzInv (0 ms) 60: [ RUN ] SimdMathTest.cbrt 60: [ OK ] SimdMathTest.cbrt (0 ms) 60: [ RUN ] SimdMathTest.invcbrt 60: [ OK ] SimdMathTest.invcbrt (1 ms) 60: [ RUN ] SimdMathTest.log2 60: [ OK ] SimdMathTest.log2 (0 ms) 60: [ RUN ] SimdMathTest.log 60: [ OK ] SimdMathTest.log (0 ms) 60: [ RUN ] SimdMathTest.exp2 60: [ OK ] SimdMathTest.exp2 (2 ms) 60: [ RUN ] SimdMathTest.exp2Unsafe 60: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 60: [ RUN ] SimdMathTest.exp 60: [ OK ] SimdMathTest.exp (2 ms) 60: [ RUN ] SimdMathTest.expUnsafe 60: [ OK ] SimdMathTest.expUnsafe (0 ms) 60: [ RUN ] SimdMathTest.pow 60: [ OK ] SimdMathTest.pow (0 ms) 60: [ RUN ] SimdMathTest.powUnsafe 60: [ OK ] SimdMathTest.powUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erf 60: [ OK ] SimdMathTest.erf (0 ms) 60: [ RUN ] SimdMathTest.erfc 60: [ OK ] SimdMathTest.erfc (0 ms) 60: [ RUN ] SimdMathTest.sin 60: [ OK ] SimdMathTest.sin (0 ms) 60: [ RUN ] SimdMathTest.cos 60: [ OK ] SimdMathTest.cos (0 ms) 60: [ RUN ] SimdMathTest.tan 60: [ OK ] SimdMathTest.tan (1 ms) 60: [ RUN ] SimdMathTest.asin 60: [ OK ] SimdMathTest.asin (0 ms) 60: [ RUN ] SimdMathTest.acos 60: [ OK ] SimdMathTest.acos (0 ms) 60: [ RUN ] SimdMathTest.atan 60: [ OK ] SimdMathTest.atan (0 ms) 60: [ RUN ] SimdMathTest.atan2 60: [ OK ] SimdMathTest.atan2 (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrection 60: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrection 60: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracy 60: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.invSingleAccuracy 60: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.cbrtSingleAccuracy 60: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 60: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 60: [ RUN ] SimdMathTest.log2SingleAccuracy 60: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.logSingleAccuracy 60: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracy 60: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 60: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracy 60: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracy 60: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erfSingleAccuracy 60: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.erfcSingleAccuracy 60: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sinSingleAccuracy 60: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.cosSingleAccuracy 60: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.tanSingleAccuracy 60: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.asinSingleAccuracy 60: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.acosSingleAccuracy 60: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atanSingleAccuracy 60: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atan2SingleAccuracy 60: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 56 tests from SimdMathTest (34 ms total) 60: 60: [----------] 1 test from EmptyArrayRefTest 60: [ RUN ] EmptyArrayRefTest.IsEmpty 60: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 60: [----------] 1 test from EmptyArrayRefTest (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/0.Assignment 60: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/1.Assignment 60: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/0.Basic 60: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/1.Basic 60: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 60: 60: [----------] 3 tests from SimdVectorOperationsTest 60: [ RUN ] SimdVectorOperationsTest.iprod 60: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 60: [ RUN ] SimdVectorOperationsTest.norm2 60: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 60: [ RUN ] SimdVectorOperationsTest.cprod 60: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 60: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 247 tests from 19 test suites ran. (35 ms total) 60: [ PASSED ] 247 tests. 60/104 Test #60: SimdUnitTests ............................. Passed 0.05 sec test 61 Start 61: CompatibilityHelpersTests 61: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/compat/tests 61: Test timeout computed to be: 30 61: [==========] Running 9 tests from 6 test suites. 61: [----------] Global test environment set-up. 61: [----------] 4 tests from TemplateMPTest 61: [ RUN ] TemplateMPTest.MpWithIndexInt 61: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexIntBad 61: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexBool 61: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexEnum 61: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 61: [----------] 4 tests from TemplateMPTest (0 ms total) 61: 61: [----------] 1 test from NotNullConstruction 61: [ RUN ] NotNullConstruction.Works 61: [ OK ] NotNullConstruction.Works (0 ms) 61: [----------] 1 test from NotNullConstruction (0 ms total) 61: 61: [----------] 1 test from NotNullCasting 61: [ RUN ] NotNullCasting.Works 61: [ OK ] NotNullCasting.Works (0 ms) 61: [----------] 1 test from NotNullCasting (0 ms total) 61: 61: [----------] 1 test from NotNullAssignment 61: [ RUN ] NotNullAssignment.Works 61: [ OK ] NotNullAssignment.Works (0 ms) 61: [----------] 1 test from NotNullAssignment (0 ms total) 61: 61: [----------] 1 test from MakeNotNull 61: [ RUN ] MakeNotNull.Works 61: [ OK ] MakeNotNull.Works (0 ms) 61: [----------] 1 test from MakeNotNull (0 ms total) 61: 61: [----------] 1 test from NotNull 61: [ RUN ] NotNull.WorksInContainers 61: [ OK ] NotNull.WorksInContainers (0 ms) 61: [----------] 1 test from NotNull (0 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 9 tests from 6 test suites ran. (0 ms total) 61: [ PASSED ] 9 tests. 61/104 Test #61: CompatibilityHelpersTests ................. Passed 0.01 sec test 62 Start 62: GmxAnaTest 62: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 62: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests 62: Test timeout computed to be: 600 62: [==========] Running 37 tests from 10 test suites. 62: [----------] Global test environment set-up. 62: [----------] 7 tests from Entropy 62: [ RUN ] Entropy.Schlitter_300_NoLinear 62: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 62: [ RUN ] Entropy.Schlitter_300_Linear 62: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_Linear 62: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 62: [ RUN ] Entropy.EntropyCompare_200_Linear 62: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 62: [ RUN ] Entropy.EntropyCompare_300_Linear 62: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 62: [----------] 7 tests from Entropy (0 ms total) 62: 62: [----------] 2 tests from GmxChiTest 62: [ RUN ] GmxChiTest.gmxchiWorksWithAll 62: Analyzing from residue 1 to residue 11 62: 10 residues with dihedrals found 62: 46 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 46 62: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithAll (405 ms) 62: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 62: Analyzing from residue 2 to residue 6 62: 5 residues with dihedrals found 62: 23 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 23 62: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (177 ms) 62: [----------] 2 tests from GmxChiTest (642 ms total) 62: 62: [----------] 10 tests from MindistTest 62: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistWorksWithSingleAtoms (5 ms) 62: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 62: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 62: [ RUN ] MindistTest.mindistPicksUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 62: [ RUN ] MindistTest.ngWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.ngWorks (0 ms) 62: [ RUN ] MindistTest.groupWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.groupWorks (1 ms) 62: [ RUN ] MindistTest.maxDistWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.maxDistWorks (0 ms) 62: [ RUN ] MindistTest.noPbcWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.noPbcWorks (0 ms) 62: [ RUN ] MindistTest.resPerTimeWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.resPerTimeWorks (0 ms) 62: [ RUN ] MindistTest.matrixWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 5: 'atoms123' 62: Special case: making distance matrix between all atoms in group atoms123 62: [ OK ] MindistTest.matrixWorks (0 ms) 62: [----------] 10 tests from MindistTest (11 ms total) 62: 62: [----------] 1 test from GmxRmsTest 62: [ RUN ] GmxRmsTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Select group for least squares fit 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Select group for RMSD calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to -537438209 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 1: 'Protein' 62: Selected 1: 'Protein' 62: [ OK ] GmxRmsTest.BasicOutputWorks (264 ms) 62: [----------] 1 test from GmxRmsTest (264 ms total) 62: 62: [----------] 1 test from GmxRmsdistTest 62: [ RUN ] GmxRmsdistTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: 62: rmsmax = 0.382568, rmscmax = 0.659498 62: Setting the LD random seed to 1072670706 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 0: 'System' 62: [ OK ] GmxRmsdistTest.BasicOutputWorks (264 ms) 62: [----------] 1 test from GmxRmsdistTest (264 ms total) 62: 62: [----------] 1 test from GmxRmsfTest 62: [ RUN ] GmxRmsfTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Select group(s) for root mean square calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to -1094721539 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 3: 'C-alpha' 62: [ OK ] GmxRmsfTest.BasicOutputWorks (253 ms) 62: [----------] 1 test from GmxRmsfTest (253 ms total) 62: 62: [----------] 1 test from GmxSorientTest 62: [ RUN ] GmxSorientTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Group 0 ( System) has 923 elements 62: Group 1 ( Protein) has 29 elements 62: Group 2 ( Protein-H) has 17 elements 62: Group 3 ( C-alpha) has 2 elements 62: Group 4 ( Backbone) has 6 elements 62: Group 5 ( MainChain) has 9 elements 62: Group 6 ( MainChain+Cb) has 11 elements 62: Group 7 ( MainChain+H) has 13 elements 62: Group 8 ( SideChain) has 16 elements 62: Group 9 ( SideChain-H) has 8 elements 62: Group 10 ( Prot-Masses) has 23 elements 62: Group 11 ( non-Protein) has 894 elements 62: Group 12 ( Water) has 894 elements 62: Group 13 ( SOL) has 894 elements 62: Group 14 ( non-Water) has 29 elements 62: Select a group: Select a group: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Average nr of molecules between 0 and 0.5 nm: 13.0 62: Average cos(theta1) between 0 and 0.5 nm: 0.103 62: Average 3cos2(theta2)-1 between 0 and 0.5 nm: -0.098 62: Setting the LD random seed to -375406593 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.pdb', all velocities are zero 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: Analysing residue names: 62: There are: 2 Protein residues 62: There are: 298 Water residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Select a group of reference particles and a solvent group: 62: Selected 1: 'Protein' 62: Selected 12: 'Water' 62: [ OK ] GmxSorientTest.BasicOutputWorks (14 ms) 62: [----------] 1 test from GmxSorientTest (14 ms total) 62: 62: [----------] 1 test from GmxRotmatTest 62: [ RUN ] GmxRotmatTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Setting the LD random seed to -864026721 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 4: 'Backbone' 62: [ OK ] GmxRotmatTest.BasicOutputWorks (255 ms) 62: [----------] 1 test from GmxRotmatTest (255 ms total) 62: 62: [----------] 1 test from GmxSaltbrTest 62: [ RUN ] GmxSaltbrTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Setting the LD random seed to -1718436897 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: This run will generate roughly 0 Mb of data 62: CG: SOL1-1 Q: -0.834 Atoms: 0 62: CG: SOL1-2 Q: 0.417 Atoms: 1 62: CG: SOL1-3 Q: 0.417 Atoms: 2 62: CG: SOL2-4 Q: -0.834 Atoms: 3 62: CG: SOL2-5 Q: 0.417 Atoms: 4 62: CG: SOL2-6 Q: 0.417 Atoms: 5 62: [ OK ] GmxSaltbrTest.BasicOutputWorks (3 ms) 62: [----------] 1 test from GmxSaltbrTest (3 ms total) 62: 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (0 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (12 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 37 tests from 10 test suites ran. (1725 ms total) 62: [ PASSED ] 37 tests. 62/104 Test #62: GmxAnaTest ................................ Passed 1.74 sec test 63 Start 63: GmxPreprocessTests 63: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 63: Test timeout computed to be: 1920 63: [==========] Running 237 tests from 16 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertInteractionsTest 63: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 63: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 63: [----------] 1 test from ConvertInteractionsTest (0 ms total) 63: 63: [----------] 5 tests from GenconfTest 63: [ RUN ] GenconfTest.nbox_Works 63: [ OK ] GenconfTest.nbox_Works (0 ms) 63: [ RUN ] GenconfTest.nbox_norenumber_Works 63: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 63: [ RUN ] GenconfTest.nbox_dist_Works 63: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 63: [ RUN ] GenconfTest.nbox_rot_Works 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 63: [ RUN ] GenconfTest.trj_Works 63: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 63: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Last frame 3 time 3.000 63: [ OK ] GenconfTest.trj_Works (0 ms) 63: [----------] 5 tests from GenconfTest (2 ms total) 63: 63: [----------] 2 tests from GenionTest 63: [ RUN ] GenionTest.HighConcentrationIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Group 0 ( System) has 653 elements 63: Group 1 ( Water) has 648 elements 63: Group 2 ( SOL) has 648 elements 63: Group 3 ( non-Water) has 5 elements 63: Group 4 ( Other) has 5 elements 63: Group 5 ( METH) has 5 elements 63: Select a group: Number of (3-atomic) solvent molecules: 216 63: Using random seed 1997. 63: Replacing solvent molecule 56 (atom 168) with NA 63: Replacing solvent molecule 120 (atom 360) with NA 63: Replacing solvent molecule 182 (atom 546) with NA 63: Replacing solvent molecule 71 (atom 213) with NA 63: Replacing solvent molecule 189 (atom 567) with CL 63: Replacing solvent molecule 54 (atom 162) with CL 63: Replacing solvent molecule 155 (atom 465) with CL 63: Replacing solvent molecule 99 (atom 297) with CL 63: 63: Setting the LD random seed to -8519681 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: Will try to add 4 NA ions and 4 CL ions. 63: Select a continuous group of solvent molecules 63: Selected 1: 'Water' 63: [ OK ] GenionTest.HighConcentrationIonPlacement (326 ms) 63: [ RUN ] GenionTest.NoIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: No ions to add, will just copy input configuration. 63: Setting the LD random seed to -556142731 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GenionTest.NoIonPlacement (266 ms) 63: [----------] 2 tests from GenionTest (593 ms total) 63: 63: [----------] 1 test from GenRestrTest 63: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 63: 63: Reading structure file 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Select group to position restrain 63: Selected 3: 'C-alpha' 63: [ OK ] GenRestrTest.SimpleRestraintsGenerated (0 ms) 63: [----------] 1 test from GenRestrTest (1 ms total) 63: 63: [----------] 9 tests from PreprocessingAtomTypesTest 63: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 63: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 63: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 63: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 63: 63: [----------] 10 tests from PreprocessingBondAtomTypeTest 63: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 63: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 63: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 63: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 63: 63: [----------] 3 tests from GromppDirectiveTest 63: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -89817473 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1115718809 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (2 ms) 63: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 63: coefficients that do not sum to zero. This does not affect the simulation 63: and can be ignored, unless you are comparing potential energy values with 63: other force field ports and/or MD software. 63: First such dihedral in molecule A, involving atoms 0 2 1 3 63: 63: 63: NOTE 2 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to 1946156861 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -568410115 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (2 ms) 63: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 63: Setting the LD random seed to 1711275387 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 534248444 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (5 ms) 63: [----------] 3 tests from GromppDirectiveTest (11 ms total) 63: 63: [----------] 6 tests from InsertMoleculesTest 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: 63: Added 1 molecules (out of 1 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 63: 63: Output configuration contains 8 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (0 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (0 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: Try 2 success (now 10 atoms)! 63: 63: Added 2 molecules (out of 2 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 63: 63: Output configuration contains 10 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 650 atoms)! 63: Try 2 success (now 652 atoms)! 63: Try 3 success (now 654 atoms)! 63: Try 4 success (now 656 atoms)! 63: 63: Added 4 molecules (out of 4 requested) 63: Replaced 8 residues (24 atoms) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 63: 63: Output configuration contains 632 atoms in 212 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (2 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Read 4 positions from file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 63: 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 63: Try 13 success (now 6 atoms)! 63: 63: Added 3 molecules (out of 4 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 63: 63: Output configuration contains 6 atoms in 3 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (0 ms) 63: [----------] 6 tests from InsertMoleculesTest (6 ms total) 63: 63: [----------] 3 tests from MassRepartitioning 63: [ RUN ] MassRepartitioning.ValidCaseWorks 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 63: [ RUN ] MassRepartitioning.UnboundGivesWarning 63: 63: WARNING 1 [file unknown]: 63: The are 1 atoms that have a mass below the mass repartitioning limit but 63: are not bound. These masses cannot be repartitioned. 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 63: [ RUN ] MassRepartitioning.LightPartnerGivesError 63: 63: ERROR 1 [file unknown]: 63: Light atoms are bound to at least one atom that has a too low mass for 63: repartitioning 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 63: [----------] 3 tests from MassRepartitioning (0 ms total) 63: 63: [----------] 36 tests from GetIrTest 63: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 63: Ignoring obsolete mdp entry 'title' 63: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (1 ms) 63: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 63: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (3 ms) 63: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) 63: [ RUN ] GetIrTest.RejectsValueWithoutKey 63: [ OK ] GetIrTest.RejectsValueWithoutKey (3 ms) 63: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 63: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (3 ms) 63: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 63: [ RUN ] GetIrTest.AcceptsEmptyLines 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstpcouple 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: With multiple time stepping, nstpcouple should be a multiple of 63: mts-factor 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: The Berendsen barostat does not generate any strictly correct ensemble, 63: and should not be used for new production simulations (in our opinion). 63: We recommend using the C-rescale barostat instead. 63: 63: 63: ERROR 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: compressibility must be > 0 when using pressure coupling Berendsen 63: 63: 63: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstdhdl 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstdhdl (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Lambda state must be set, either with init-lambda-state or with 63: init-lambda 63: 63: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 63: [ RUN ] GetIrTest.MtsCheckSDNotSupported 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: Multiple time stepping is only supported with integrator md 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 63: [ RUN ] GetIrTest.AcceptsElectricField 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricField (1 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 63: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 63: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (2 ms) 63: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 63: [ RUN ] GetIrTest.RejectsImplicitSolventYes 63: [ OK ] GetIrTest.RejectsImplicitSolventYes (3 ms) 63: [ RUN ] GetIrTest.AcceptsMimic 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsMimic (1 ms) 63: [ RUN ] GetIrTest.AcceptsTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 63: pull-coord2 has a non-zero force constant and is also referenced in 63: pull-coord1-expression. Make sure that this is intended. In most use 63: cases, the pull coordinates referenced by a transformation coordinate 63: should have their force constant set to zero. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 63: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 63: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 63: pull-coord2 can not use pull-coord1 in the transformation since this is a 63: constraint 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 63: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 63: [ RUN ] GetIrTest.MissingTransformationCoordExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 63: pull-coord1-expression not set for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 63: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 63: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 63: in total 100001 steps. This is not compatible with using soft-core 63: potentials. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 63: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.AcceptsFmmOptions 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsFmmOptions_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsFmmOptions (1 ms) 63: [----------] 36 tests from GetIrTest (64 ms total) 63: 63: [----------] 6 tests from SolvateTest 63: [ RUN ] SolvateTest.cs_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 1x1x1 boxes 63: Solvent box contains 270 atoms in 90 residues 63: Removed 129 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 47 residues 63: Generated solvent containing 141 atoms in 47 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 63: 63: Output configuration contains 141 atoms in 47 residues 63: Volume : 1.331 (nm^3) 63: Density : 1056.36 (g/l) 63: Number of solvent molecules: 47 63: 63: [ OK ] SolvateTest.cs_box_Works (2 ms) 63: [ RUN ] SolvateTest.cs_cp_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: [ OK ] SolvateTest.cs_cp_Works (12 ms) 63: [ RUN ] SolvateTest.cs_cp_p_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: Processing topology 63: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 63: [ OK ] SolvateTest.cs_cp_p_Works (15 ms) 63: [ RUN ] SolvateTest.shell_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 1902 solvent atoms more than 1.000000 nm from solute. 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 252 residues 63: Generated solvent containing 756 atoms in 252 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 63: 63: Output configuration contains 762 atoms in 254 residues 63: Volume : 27.2709 (nm^3) 63: Density : 279.3 (g/l) 63: Number of solvent molecules: 252 63: 63: [ OK ] SolvateTest.shell_Works (7 ms) 63: [ RUN ] SolvateTest.update_Topology_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 3x3x3 boxes 63: Solvent box contains 14952 atoms in 4984 residues 63: Removed 2787 solvent atoms due to solvent-solvent overlap 63: Removed 30 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 2 different molecule types: 63: HOH ( 3 atoms): 1876 residues 63: SOL ( 3 atoms): 2169 residues 63: Generated solvent containing 0 atoms in 0 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 63: 63: Output configuration contains 12141 atoms in 4047 residues 63: Volume : 125 (nm^3) 63: Density : 968.963 (g/l) 63: Number of solvent molecules: 4045 63: 63: Processing topology 63: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: [ OK ] SolvateTest.update_Topology_Works (53 ms) 63: [ RUN ] SolvateTest.cs_pdb_big_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 1218 atoms in 406 residues 63: Removed 555 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 221 residues 63: Generated solvent containing 663 atoms in 221 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 63: 63: Output configuration contains 663 atoms in 221 residues 63: Volume : 8 (nm^3) 63: Density : 826.409 (g/l) 63: Number of solvent molecules: 221 63: 63: [ OK ] SolvateTest.cs_pdb_big_box_Works (7 ms) 63: [----------] 6 tests from SolvateTest (99 ms total) 63: 63: [----------] 1 test from TopDirTests 63: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 63: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 63: [----------] 1 test from TopDirTests (0 ms total) 63: 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (1 ms total) 63: 63: [----------] 16 tests from CorrectVelocity/MaxwellTest 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 63: [----------] 16 tests from CorrectVelocity/MaxwellTest (13 ms total) 63: 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -302094341 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2146172863 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -1115693057 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2129448951 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -591429674 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1644282313 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -57279785 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 734003183 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to 956294719 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -830493829 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -1176781449 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1283 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -554852354 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 982457314 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -629549059 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1409352773 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -152617093 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -38404681 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to 1047461154 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1229990417 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -323224649 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -69731381 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -404949026 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -541070491 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -176685508 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -541711 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -1113719813 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1875377469 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -12599851 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to 1535096831 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -1737262 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -134284322 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -1480606353 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -171409433 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to -1074012434 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -28933 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 63: Setting the LD random seed to 1909384703 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -258 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 (2 ms) 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest (64 ms total) 63: 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 63: Setting the LD random seed to -1493766677 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (5 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 63: Setting the LD random seed to -65537 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -59901221 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -806363697 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -195605079 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -134316115 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -1250121729 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -402661635 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -411568165 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -209731716 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 63: Setting the LD random seed to -2172209 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 63: Setting the LD random seed to 2145255166 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1809841151 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (5 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 63: Setting the LD random seed to 1593733109 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 63: Setting the LD random seed to -672231425 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2070937435 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 63: Setting the LD random seed to -283122945 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2008022654 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 63: Setting the LD random seed to 921361405 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1886046049 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (5 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 63: Setting the LD random seed to -8398564 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -4628 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 63: Setting the LD random seed to -34404993 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -29886789 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 63: Setting the LD random seed to 1474289045 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1376922953 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 63: Setting the LD random seed to -1075848274 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1646583811 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (5 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -579738691 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1612775553 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -1049123 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -202395721 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 63: Setting the LD random seed to -12600413 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 63: Setting the LD random seed to 2104970751 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -16908481 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (5 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 63: Setting the LD random seed to -1419784259 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -25755937 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -10649651 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 63: Setting the LD random seed to -551 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 63: Setting the LD random seed to -34147457 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1739259695 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 (4 ms) 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest (99 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 237 tests from 16 test suites ran. (959 ms total) 63: [ PASSED ] 197 tests. 63: [ SKIPPED ] 40 tests, listed below: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63/104 Test #63: GmxPreprocessTests ........................ Passed 0.98 sec test 64 Start 64: Pdb2gmx1Test 64: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 64: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 64: Test timeout computed to be: 1920 64: [==========] Running 30 tests from 1 test suite. 64: [----------] Global test environment set-up. 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (16 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (12 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (38 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (14 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest (592 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 30 tests from 1 test suite ran. (592 ms total) 64: [ PASSED ] 30 tests. 64/104 Test #64: Pdb2gmx1Test .............................. Passed 0.60 sec test 65 Start 65: Pdb2gmx2Test 65: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 65: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 65: Test timeout computed to be: 1920 65: [==========] Running 40 tests from 2 test suites. 65: [----------] Global test environment set-up. 65: [----------] 20 tests from G43a1/Pdb2gmxTest 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (15 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (31 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (32 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (31 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (34 ms) 65: [----------] 20 tests from G43a1/Pdb2gmxTest (399 ms total) 65: 65: [----------] 20 tests from G53a6/Pdb2gmxTest 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (35 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (35 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (33 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (33 ms) 65: [----------] 20 tests from G53a6/Pdb2gmxTest (443 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 40 tests from 2 test suites ran. (842 ms total) 65: [ PASSED ] 40 tests. 65/104 Test #65: Pdb2gmx2Test .............................. Passed 0.85 sec test 66 Start 66: Pdb2gmx3Test 66: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 66: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 66: Test timeout computed to be: 1920 66: [==========] Running 55 tests from 9 test suites. 66: [----------] Global test environment set-up. 66: [----------] 10 tests from Amber/Pdb2gmxTest 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (49 ms) 66: [----------] 10 tests from Amber/Pdb2gmxTest (258 ms total) 66: 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest 66: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber99sb-ildn.ff/rna.arn 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber99sb-ildn force field and the tip4p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (9 ms) 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest (9 ms total) 66: 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (16 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (38 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (16 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (13 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (38 ms) 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest (196 ms total) 66: 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the opc water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (7 ms) 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the tip4pew water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (6 ms) 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest (14 ms total) 66: 66: [----------] 12 tests from Charmm/Pdb2gmxTest 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 0 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Marked 8 virtual sites 66: Added 2 dummy masses 66: Added 3 new constraints 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 9 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 66: [----------] 12 tests from Charmm/Pdb2gmxTest (262 ms total) 66: 66: [----------] 8 tests from ChainSep/Pdb2gmxTest 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (17 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 7 acceptors were found. 66: There are 7 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS8 66: NE223 66: MET12 SD55 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 317 pairs 66: Before cleaning: 322 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 7 58 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (58 atoms, 7 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 124 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 125, now 125 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 5 cmap torsion pairs 66: 66: There are 322 dihedrals, 19 impropers, 227 angles 66: 314 pairs, 125 bonds and 0 virtual sites 66: 66: Total mass 846.083 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 124 atoms 7 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (16 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (19 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 12 acceptors were found. 66: There are 13 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 66: SG9 66: HIS8 NE251 1.055 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 288 pairs 66: Before cleaning: 293 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 8 61 66: 66: 2 'B' 3 25 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (61 atoms, 8 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 8 residues with 114 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 115, now 115 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6 cmap torsion pairs 66: 66: There are 293 dihedrals, 23 impropers, 203 angles 66: 285 pairs, 115 bonds and 0 virtual sites 66: 66: Total mass 888.952 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 114 atoms 8 residues 66: 66: Including chain 2 in system: 61 atoms 3 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (19 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 650 pairs 66: Before cleaning: 660 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 3 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 261 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 260, now 260 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 8 cmap torsion pairs 66: 66: There are 660 dihedrals, 45 impropers, 466 angles 66: 647 pairs, 260 bonds and 0 virtual sites 66: 66: Total mass 1900.162 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (17 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 6 donors and 4 acceptors were found. 66: There are 3 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 164 pairs 66: Before cleaning: 169 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 4 33 66: 66: 3 'B' 3 25 66: 66: 4 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (33 atoms, 4 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 66 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 67, now 67 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 169 dihedrals, 13 impropers, 118 angles 66: 161 pairs, 67 bonds and 0 virtual sites 66: 66: Total mass 472.547 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 4 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 66 atoms 4 residues 66: 66: Including chain 3 in system: 61 atoms 3 residues 66: 66: Including chain 4 in system: 83 atoms 5 residues 66: 66: Now there are 261 atoms and 16 residues 66: 66: Total mass in system 1900.162 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 652 pairs 66: Before cleaning: 662 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 256, now 256 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 12 cmap torsion pairs 66: 66: There are 662 dihedrals, 47 impropers, 460 angles 66: 649 pairs, 256 bonds and 0 virtual sites 66: 66: Total mass 1864.131 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (18 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 14 donors and 15 acceptors were found. 66: There are 20 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 441 pairs 66: Before cleaning: 446 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 11 86 66: 66: 2 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (86 atoms, 11 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 11 residues with 172 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 173, now 173 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 9 cmap torsion pairs 66: 66: There are 446 dihedrals, 29 impropers, 312 angles 66: 438 pairs, 173 bonds and 0 virtual sites 66: 66: Total mass 1262.488 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 172 atoms 11 residues 66: 66: Including chain 2 in system: 83 atoms 5 residues 66: 66: Now there are 255 atoms and 16 residues 66: 66: Total mass in system 1864.131 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (15 ms) 66: [----------] 8 tests from ChainSep/Pdb2gmxTest (143 ms total) 66: 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest (52 ms total) 66: 66: [----------] 4 tests from Cyclic/Pdb2gmxTest 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: Moved all the water blocks to the end 66: 66: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 71 1527 66: 66: 2 'Q' 71 1527 66: 66: 3 'Q' 7 7 66: 66: 4 ' ' 10 10 (only water) 66: 66: 5 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'Q' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'Q' (7 atoms, 7 residues) 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 7 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: No bonds 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 0 angles 66: 0 pairs, 0 bonds and 0 virtual sites 66: 66: Total mass 170.135 a.m.u. 66: 66: Total charge 14.000 e 66: 66: Writing topology 66: 66: Processing chain 4 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 5 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain m9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: olecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 2297 atoms 71 residues 66: 66: Including chain 2 in system: 2297 atoms 71 residues 66: 66: Including chain 3 in system: 7 atoms 7 residues 66: 66: Including chain 4 in system: 30 atoms 10 residues 66: 66: Including chain 5 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.563 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (217 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (41 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 12080 pairs 66: Before cleaning: 13210 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Moved all the water blocks to the end 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 149 3061 66: 66: 2 ' ' 10 10 (only water) 66: 66: 3 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (3061 atoms, 149 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 149 residues with 4601 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4962, now 4962 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 13210 dihedrals, 366 impropers, 8868 angles 66: 11654 pairs, 4962 bonds and 0 virtual sites 66: 66: Total mass 46139.162 a.m.u. 66: 66: Total charge -128.000 e 66: 66: Writing topology 66: 66: Processing chain 2 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 3 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 4601 atoms 149 residues 66: 66: Including chain 2 in system: 30 atoms 10 residues 66: 66: Including chain 3 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.563 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (240 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (39 ms) 66: [----------] 4 tests from Cyclic/Pdb2gmxTest (538 ms total) 66: 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 5 47 66: 66: 2 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2325 dihedrals, 141 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.100 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 86 atoms 5 residues 66: 66: Including chain 2 in system: 878 atoms 60 residues 66: 66: Now there are 964 atoms and 65 residues 66: 66: Total mass in system 6519.802 a.m.u. 66: 66: Total charge in system 4.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file (47 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 188 pairs 66: Before cleaning: 198 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 3 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 4 38 66: 66: 2 'E' 5 47 66: 66: 3 'F' 5 47 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (38 atoms, 4 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 72 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 75, now 74 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 198 dihedrals, 18 impropers, 132 angles 66: 185 pairs, 74 bonds and 0 virtual sites 66: 66: Total mass 543.584 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'E' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'F' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 72 atoms 4 residues 66: 66: Including chain 2 in system: 86 atoms 5 residues 66: 66: Including chain 3 in system: 86 atoms 5 residues 66: 66: Now there are 244 atoms and 14 residues 66: 66: Total mass in system 1850.988 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file (21 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 2558 pairs 66: Before cleaning: 2568 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 65 460 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (460 atoms, 65 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 65 residues with 964 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 969, now 969 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2568 dihedrals, 164 impropers, 1773 angles 66: 2549 pairs, 969 bonds and 0 virtual sites 66: 66: Total mass 6519.802 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file (45 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.1/share/top/amber96.ff/rna.arn 66: Before cleaning: 654 pairs 66: Before cleaning: 684 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 14 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (132 atoms, 14 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 14 residues with 244 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 253, now 252 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 684 dihedrals, 64 impropers, 450 angles 66: 645 pairs, 252 bonds and 0 virtual sites 66: 66: Total mass 1850.988 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.1/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file (19 ms) 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest (133 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 55 tests from 9 test suites ran. (1610 ms total) 66: [ PASSED ] 55 tests. 66/104 Test #66: Pdb2gmx3Test .............................. Passed 1.62 sec test 67 Start 67: CorrelationsTest 67: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 67: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/correlationfunctions/tests 67: Test timeout computed to be: 30 67: [==========] Running 21 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 10 tests from AutocorrTest 67: [ RUN ] AutocorrTest.EacNormal 67: [ OK ] AutocorrTest.EacNormal (15 ms) 67: [ RUN ] AutocorrTest.EacNoNormalize 67: [ OK ] AutocorrTest.EacNoNormalize (7 ms) 67: [ RUN ] AutocorrTest.EacCos 67: [ OK ] AutocorrTest.EacCos (18 ms) 67: [ RUN ] AutocorrTest.EacVector 67: [ OK ] AutocorrTest.EacVector (23 ms) 67: [ RUN ] AutocorrTest.EacRcross 67: [ OK ] AutocorrTest.EacRcross (1 ms) 67: [ RUN ] AutocorrTest.EacP0 67: [ OK ] AutocorrTest.EacP0 (19 ms) 67: [ RUN ] AutocorrTest.EacP1 67: [ OK ] AutocorrTest.EacP1 (20 ms) 67: [ RUN ] AutocorrTest.EacP2 67: [ OK ] AutocorrTest.EacP2 (45 ms) 67: [ RUN ] AutocorrTest.EacP3 67: [ OK ] AutocorrTest.EacP3 (1 ms) 67: [ RUN ] AutocorrTest.EacP4 67: [ OK ] AutocorrTest.EacP4 (28 ms) 67: [----------] 10 tests from AutocorrTest (184 ms total) 67: 67: [----------] 10 tests from ExpfitTest 67: [ RUN ] ExpfitTest.EffnEXP1 67: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 67: [ RUN ] ExpfitTest.EffnEXP2 67: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 67: [ RUN ] ExpfitTest.EffnEXPEXP 67: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 67: [ RUN ] ExpfitTest.EffnEXP5 67: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP7 67: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP9 67: [ OK ] ExpfitTest.EffnEXP9 (6 ms) 67: [ RUN ] ExpfitTest.EffnERF 67: [ OK ] ExpfitTest.EffnERF (1 ms) 67: [ RUN ] ExpfitTest.EffnERREST 67: [ OK ] ExpfitTest.EffnERREST (1 ms) 67: [ RUN ] ExpfitTest.EffnVAC 67: [ OK ] ExpfitTest.EffnVAC (3 ms) 67: [ RUN ] ExpfitTest.EffnPRES 67: [ OK ] ExpfitTest.EffnPRES (7 ms) 67: [----------] 10 tests from ExpfitTest (24 ms total) 67: 67: [----------] 1 test from ManyAutocorrelationTest 67: [ RUN ] ManyAutocorrelationTest.Empty 67: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 67: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 21 tests from 3 test suites ran. (211 ms total) 67: [ PASSED ] 21 tests. 67/104 Test #67: CorrelationsTest .......................... Passed 0.22 sec test 68 Start 68: AnalysisDataUnitTests 68: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/analysisdata/tests 68: Test timeout computed to be: 30 68: [==========] Running 69 tests from 14 test suites. 68: [----------] Global test environment set-up. 68: [----------] 3 tests from AnalysisDataInitializationTest 68: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 68: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 68: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 68: 68: [----------] 4 tests from AnalysisArrayDataTest 68: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 68: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisArrayDataTest.StorageWorks 68: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 68: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 68: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 68: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 68: 68: [----------] 6 tests from AverageModuleTest 68: [ RUN ] AverageModuleTest.BasicTest 68: [ OK ] AverageModuleTest.BasicTest (0 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipointData 68: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 68: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 68: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeXAxis 68: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 68: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 68: [----------] 6 tests from AverageModuleTest (1 ms total) 68: 68: [----------] 2 tests from FrameAverageModuleTest 68: [ RUN ] FrameAverageModuleTest.BasicTest 68: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 68: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 68: 68: [----------] 7 tests from AnalysisHistogramSettingsTest 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 68: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 68: 68: [----------] 2 tests from SimpleHistogramModuleTest 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 68: 68: [----------] 3 tests from WeightedHistogramModuleTest 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 68: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 68: 68: [----------] 3 tests from BinAverageModuleTest 68: [ RUN ] BinAverageModuleTest.ComputesCorrectly 68: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 68: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from BinAverageModuleTest (1 ms total) 68: 68: [----------] 4 tests from AbstractAverageHistogramTest 68: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 68: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 68: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 68: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 68: 68: [----------] 3 tests from LifetimeModuleTest 68: [ RUN ] LifetimeModuleTest.BasicTest 68: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 68: [ RUN ] LifetimeModuleTest.CumulativeTest 68: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 68: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 68: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from LifetimeModuleTest (0 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 69 tests from 14 test suites ran. (12 ms total) 68: [ PASSED ] 69 tests. 68/104 Test #68: AnalysisDataUnitTests ..................... Passed 0.02 sec test 69 Start 69: CoordinateIOTests 69: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/coordinateio/tests 69: Test timeout computed to be: 30 69: [==========] Running 67 tests from 20 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from OutputSelectorDeathTest 69: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (2 ms) 69: [----------] 1 test from OutputSelectorDeathTest (2 ms total) 69: 69: [----------] 5 tests from TrajectoryFrameWriterTest 69: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 69: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 69: [----------] 5 tests from TrajectoryFrameWriterTest (4 ms total) 69: 69: [----------] 5 tests from OutputAdapterContainer 69: [ RUN ] OutputAdapterContainer.MakeEmpty 69: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 69: [ RUN ] OutputAdapterContainer.AddAdapter 69: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectBadAdapter 69: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 69: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 69: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 69: [----------] 5 tests from OutputAdapterContainer (0 ms total) 69: 69: [----------] 3 tests from RegisterFrameConverterTest 69: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 69: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 69: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 69: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 69: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 69: 69: [----------] 5 tests from FlagTest 69: [ RUN ] FlagTest.CanSetSimpleFlag 69: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 69: [ RUN ] FlagTest.CanAddNewBox 69: [ OK ] FlagTest.CanAddNewBox (0 ms) 69: [ RUN ] FlagTest.SetsImplicitPrecisionChange 69: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitStartTimeChange 69: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitTimeStepChange 69: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 69: [----------] 5 tests from FlagTest (0 ms total) 69: 69: [----------] 5 tests from SetAtomsTest 69: [ RUN ] SetAtomsTest.RemovesExistingAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) 69: [ RUN ] SetAtomsTest.AddsNewAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) 69: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) 69: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 69: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (1 ms) 69: [----------] 5 tests from SetAtomsTest (5 ms total) 69: 69: [----------] 2 tests from SetBothTimeTest 69: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 69: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 69: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 69: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 69: [----------] 2 tests from SetBothTimeTest (0 ms total) 69: 69: [----------] 2 tests from SetStartTimeTest 69: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 69: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 69: [ RUN ] SetStartTimeTest.WorksWithZeroStart 69: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 69: [----------] 2 tests from SetStartTimeTest (0 ms total) 69: 69: [----------] 1 test from SetTimeStepTest 69: [ RUN ] SetTimeStepTest.SetTimeStepWorks 69: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 69: [----------] 1 test from SetTimeStepTest (0 ms total) 69: 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (6 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (3 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (2 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (8 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (3 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (2 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput (4 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 67 tests from 20 test suites ran. (43 ms total) 69: [ PASSED ] 67 tests. 69/104 Test #69: CoordinateIOTests ......................... Passed 0.05 sec test 70 Start 70: TrajectoryAnalysisUnitTests 70: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests 70: Test timeout computed to be: 1920 70: [==========] Running 394 tests from 21 test suites. 70: [----------] Global test environment set-up. 70: [----------] 11 tests from AngleModuleTest 70: [ RUN ] AngleModuleTest.ComputesSimpleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesSimpleAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesDihedrals 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system for different angles', 33 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesMultipleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 70: [ RUN ] AngleModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 70: [----------] 11 tests from AngleModuleTest (13 ms total) 70: 70: [----------] 5 tests from ClustsizeTest 70: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 2, cmax: 4, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 70: [ RUN ] ClustsizeTest.NoMolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 1, cmax: 6, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) 70: [ RUN ] ClustsizeTest.MolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 70: [ RUN ] ClustsizeTest.MolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 1, cmax: 6, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 70: [ RUN ] ClustsizeTest.MolCSize 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolCSize (1 ms) 70: [----------] 5 tests from ClustsizeTest (6 ms total) 70: 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (2 ms total) 70: 70: [----------] 4 tests from ConvertTrjModuleTest 70: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (5 ms) 70: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (0 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (0 ms) 70: [----------] 4 tests from ConvertTrjModuleTest (12 ms total) 70: 70: [----------] 6 tests from DistanceModuleTest 70: [ RUN ] DistanceModuleTest.ComputesDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 70: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 70: Number of samples: 4 70: Average distance: 1.81066 nm 70: Standard deviation: 0.79289 nm 70: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 70: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2 and res_cog x < 2.8: 70: Number of samples: 3 70: Average distance: 1.72076 nm 70: Standard deviation: 1.24839 nm 70: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: Contacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (3 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: SuccessiveContacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: ManyContacts: 70: Number of samples: 10 70: Average distance: 1.82913 nm 70: Standard deviation: 0.78478 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (3 ms) 70: [----------] 6 tests from DistanceModuleTest (14 ms total) 70: 70: [----------] 2 tests from ExtractClusterModuleTest 70: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 70: trr version: GMX_trn_file (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (1 ms) 70: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 70: [----------] 2 tests from ExtractClusterModuleTest (2 ms total) 70: 70: [----------] 2 tests from FreeVolumeModuleTest 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for 40 particles. These were set to zero. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 13 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.02 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 70: Fractional free volume 0.194 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (43 ms) 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 17 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.48 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 70: Fractional free volume 0.200 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (43 ms) 70: [----------] 2 tests from FreeVolumeModuleTest (87 ms total) 70: 70: [----------] 13 tests from MsdModuleTest 70: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 70: [ RUN ] MsdModuleTest.multipleGroupsWork 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -419775747 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.multipleGroupsWork (15 ms) 70: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.100 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 70: Analyzed 21 frames, last time 2.000 70: Setting the LD random seed to -620839937 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (15 ms) 70: [ RUN ] MsdModuleTest.trestartLessThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -112198221 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartLessThanDt (12 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -274739201 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDt (14 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1921061922 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (11 ms) 70: [ RUN ] MsdModuleTest.molTest 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to 1744823267 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.molTest (13 ms) 70: [ RUN ] MsdModuleTest.beginFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -1166020659 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.beginFit (13 ms) 70: [ RUN ] MsdModuleTest.endFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -671712323 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.endFit (13 ms) 70: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: NOTE: You provided an index file 70: /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 70: (with -n), but it was not used by any selection. 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -944125191 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (14 ms) 70: [----------] 13 tests from MsdModuleTest (130 ms total) 70: 70: [----------] 9 tests from PairDistanceModuleTest 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 70: [----------] 9 tests from PairDistanceModuleTest (10 ms total) 70: 70: [----------] 5 tests from RdfModuleTest 70: [ RUN ] RdfModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.BasicTest (11 ms) 70: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 70: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (9 ms) 70: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (10 ms) 70: [ RUN ] RdfModuleTest.CalculatesSurf 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesSurf (5 ms) 70: [ RUN ] RdfModuleTest.CalculatesXY 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesXY (12 ms) 70: [----------] 5 tests from RdfModuleTest (50 ms total) 70: 70: [----------] 5 tests from SasaModuleTest 70: [ RUN ] SasaModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.BasicTest (5 ms) 70: [ RUN ] SasaModuleTest.HandlesSelectedResidues 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesSelectedResidues (2 ms) 70: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (3 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (3 ms) 70: [----------] 5 tests from SasaModuleTest (18 ms total) 70: 70: [----------] 9 tests from SelectModuleTest 70: [ RUN ] SelectModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.BasicTest (1 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 70: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 70: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 70: [ RUN ] SelectModuleTest.NormalizesSizes 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 70: [ RUN ] SelectModuleTest.WritesResidueNumbers 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueNumbers (0 ms) 70: [ RUN ] SelectModuleTest.WritesResidueIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 70: [ RUN ] SelectModuleTest.HandlesPrimeInAtomName 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.HandlesPrimeInAtomName (1 ms) 70: [----------] 9 tests from SelectModuleTest (12 ms total) 70: 70: [----------] 10 tests from SurfaceAreaTest 70: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 70: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 70: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 70: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints12 70: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints32 70: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints42 70: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints122 70: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 70: [ RUN ] SurfaceAreaTest.Computes100Points 70: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 70: [----------] 10 tests from SurfaceAreaTest (5 ms total) 70: 70: [----------] 4 tests from TopologyInformation 70: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 70: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 70: [ RUN ] TopologyInformation.WorksWithGroFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 70: [ RUN ] TopologyInformation.WorksWithPdbFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) 70: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file lysozyme.top, line 1465]: 70: System has non-zero total charge: 2.000000 70: Total charge should normally be an integer. See 70: https://manual.gromacs.org/current/user-guide/floating-point.html 70: for discussion on how close it should be to an integer. 70: 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 465.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 70: Setting the LD random seed to -554369410 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 70: Analysing residue names: 70: There are: 10 Protein residues 70: Analysing Protein... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (284 ms) 70: [----------] 4 tests from TopologyInformation (286 ms total) 70: 70: [----------] 4 tests from TrajectoryModuleTest 70: [ RUN ] TrajectoryModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 70: [ RUN ] TrajectoryModuleTest.PlotsXOnly 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoForces 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 70: [----------] 4 tests from TrajectoryModuleTest (5 ms total) 70: 70: [----------] 5 tests from UnionFinderTest 70: [ RUN ] UnionFinderTest.WorksEmpty 70: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 70: [ RUN ] UnionFinderTest.BasicMerges 70: [ OK ] UnionFinderTest.BasicMerges (0 ms) 70: [ RUN ] UnionFinderTest.LargerMerges 70: [ OK ] UnionFinderTest.LargerMerges (0 ms) 70: [ RUN ] UnionFinderTest.LongRightMerge 70: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 70: [ RUN ] UnionFinderTest.LongLeftMerge 70: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 70: [----------] 5 tests from UnionFinderTest (0 ms total) 70: 70: [----------] 1 test from MappedUnionFinderTest 70: [ RUN ] MappedUnionFinderTest.BasicMerges 70: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 70: [----------] 1 test from MappedUnionFinderTest (0 ms total) 70: 70: [----------] 192 tests from MoleculeTests/DsspModuleTest 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (8 ms) 70: [----------] 192 tests from MoleculeTests/DsspModuleTest (2168 ms total) 70: 70: [----------] 3 tests from GyrateTests/GyrateModuleTest 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (3 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (3 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (3 ms) 70: [----------] 3 tests from GyrateTests/GyrateModuleTest (11 ms total) 70: 70: [----------] 96 tests from HBondTests/HbondModuleTest 70: [ RUN ] HBondTests/HbondModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/0 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/1 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/2 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/3 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/3 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/4 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/4 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/5 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/5 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/6 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/6 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/7 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/7 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/8 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/8 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/9 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/9 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/10 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/10 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/11 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/11 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/12 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/12 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/13 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/13 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/14 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/14 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/15 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/15 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/16 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/16 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/17 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/17 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/18 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/18 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/19 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/19 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/20 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/20 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/21 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/21 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/22 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/22 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/23 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/23 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/24 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/24 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/25 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/25 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/26 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/26 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/27 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/27 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/28 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/28 (6 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/29 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/29 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/30 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/30 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/31 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/31 (5 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/32 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/32 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/33 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/33 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/34 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/34 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/35 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/35 (28 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/36 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/36 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/37 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/37 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/38 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/38 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/39 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/39 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/40 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/40 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/41 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/41 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/42 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/42 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/43 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/43 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/44 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/44 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/45 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/45 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/46 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/46 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/47 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/47 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/48 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/48 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/49 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/49 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/50 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/50 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/51 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/51 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/52 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/52 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/53 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/53 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/54 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/54 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/55 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/55 (27 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/56 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/56 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/57 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/57 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/58 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/58 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/59 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/59 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/60 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/60 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/61 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/61 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/62 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/62 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/63 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/63 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/64 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/64 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/65 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/65 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/66 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/66 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/67 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/67 (28 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/68 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/68 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/69 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/69 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/70 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/70 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/71 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/71 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/72 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/72 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/73 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/73 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/74 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/74 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/75 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/75 (28 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/76 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/76 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/77 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/77 (28 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/78 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/78 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/79 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/79 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/80 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/80 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/81 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/81 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/82 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/82 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/83 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/83 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/84 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/84 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/85 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/85 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/86 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/86 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/87 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/87 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/88 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/88 (34 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/89 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/89 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/90 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/90 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/91 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/91 (32 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/92 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/92 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/93 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/93 (33 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/94 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/94 (31 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/95 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/95 (34 ms) 70: [----------] 96 tests from HBondTests/HbondModuleTest (2383 ms total) 70: 70: [----------] 4 tests from MoleculeTests/ScatteringModule 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (5 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (167 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (5 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (43 ms) 70: [----------] 4 tests from MoleculeTests/ScatteringModule (224 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 394 tests from 21 test suites ran. (5446 ms total) 70: [ PASSED ] 394 tests. 70/104 Test #70: TrajectoryAnalysisUnitTests ............... Passed 5.47 sec test 71 Start 71: EnergyAnalysisUnitTests 71: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests 71: Test timeout computed to be: 30 71: [==========] Running 12 tests from 5 test suites. 71: [----------] Global test environment set-up. 71: [----------] 2 tests from EnergyTermTest 71: [ RUN ] EnergyTermTest.ConstructWorks 71: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 71: [ RUN ] EnergyTermTest.AddFrameWorks 71: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 71: [----------] 2 tests from EnergyTermTest (0 ms total) 71: 71: [----------] 1 test from DhdlTest 71: [ RUN ] DhdlTest.ExtractDhdl 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 71: Note: file tpx version 110, software tpx version 138 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 71: 71: 71: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 71: [ OK ] DhdlTest.ExtractDhdl (3 ms) 71: [----------] 1 test from DhdlTest (4 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.ExtractOrires 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 71: Note: file tpx version 111, software tpx version 138 71: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 71: End your selection with 0 71: Selecting all 7 orientation restraints 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 71: [ OK ] OriresTest.ExtractOrires (4 ms) 71: [----------] 1 test from OriresTest (4 ms total) 71: 71: [----------] 5 tests from EnergyTest 71: [ RUN ] EnergyTest.ExtractEnergy 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: [ OK ] EnergyTest.ExtractEnergy (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyByNumber 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Pres. DC -268.49 3 8.52175 13.2804 (bar) 71: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyMixed 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 71: [----------] 5 tests from EnergyTest (4 ms total) 71: 71: [----------] 3 tests from ViscosityTest 71: [ RUN ] ViscosityTest.EinsteinViscosity 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosity (90 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityIntegral (11 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 71: Opened /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (11 ms) 71: [----------] 3 tests from ViscosityTest (113 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 5 test suites ran. (127 ms total) 71: [ PASSED ] 12 tests. 71/104 Test #71: EnergyAnalysisUnitTests ................... Passed 0.14 sec test 72 Start 72: ToolUnitTests 72: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests 72: Test timeout computed to be: 1920 72: [==========] Running 70 tests from 8 test suites. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from DumpTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -13116133 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] DumpTest.WorksWithTpr 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 72: inputrec: 72: integrator = md 72: tinit = 0 72: dt = 0.001 72: nsteps = 0 72: init-step = 0 72: simulation-part = 1 72: mts = false 72: mass-repartition-factor = 1 72: comm-mode = Linear 72: nstcomm = 100 72: bd-fric = 0 72: ld-seed = -13116133 72: emtol = 10 72: emstep = 0.01 72: niter = 20 72: fcstep = 0 72: nstcgsteep = 1000 72: nbfgscorr = 10 72: rtpi = 0.05 72: nstxout = 0 72: nstvout = 0 72: nstfout = 0 72: nstlog = 1000 72: nstcalcenergy = 100 72: nstenergy = 1000 72: nstxout-compressed = 0 72: compressed-x-precision = 1000 72: cutoff-scheme = Verlet 72: nstlist = 10 72: pbc = xyz 72: periodic-molecules = false 72: verlet-buffer-tolerance = -1 72: verlet-buffer-pressure-tolerance = 0.5 72: rlist = 1.1 72: coulombtype = Cut-off 72: coulomb-modifier = Potential-shift 72: rcoulomb-switch = 0 72: rcoulomb = 1 72: epsilon-r = 1 72: epsilon-rf = inf 72: vdw-type = Cut-off 72: vdw-modifier = Potential-shift 72: rvdw-switch = 0 72: rvdw = 1 72: DispCorr = No 72: table-extension = 1 72: fourierspacing = 0.12 72: fourier-nx = 0 72: fourier-ny = 0 72: fourier-nz = 0 72: pme-order = 4 72: ewald-rtol = 1e-05 72: ewald-rtol-lj = 0.001 72: lj-pme-comb-rule = Geometric 72: ewald-geometry = 3d 72: epsilon-surface = 0 72: ensemble-temperature-setting = not available 72: tcoupl = No 72: nsttcouple = -1 72: nh-chain-length = 0 72: print-nose-hoover-chain-variables = false 72: pcoupl = No 72: refcoord-scaling = No 72: posres-com: not available 72: posres-comB: not available 72: QMMM = false 72: qm-opts: 72: ngQM = 0 72: constraint-algorithm = Lincs 72: continuation = false 72: Shake-SOR = false 72: shake-tol = 0.0001 72: lincs-order = 4 72: lincs-iter = 1 72: lincs-warnangle = 30 72: nwall = 0 72: wall-type = 9-3 72: wall-r-linpot = -1 72: wall-atomtype[0] = -1 72: wall-atomtype[1] = -1 72: wall-density[0] = 0 72: wall-density[1] = 0 72: wall-ewald-zfac = 3 72: pull = false 72: awh = false 72: rotation = false 72: interactiveMD = false 72: disre = No 72: disre-weighting = Conservative 72: disre-mixed = false 72: dr-fc = 1000 72: dr-tau = 0 72: nstdisreout = 100 72: orire-fc = 0 72: orire-tau = 0 72: nstorireout = 100 72: free-energy = no 72: cos-acceleration = 0 72: deform (3x3): 72: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: simulated-tempering = false 72: swapcoords = no 72: userint1 = 0 72: userint2 = 0 72: userint3 = 0 72: userint4 = 0 72: userreal1 = 0 72: userreal2 = 0 72: userreal3 = 0 72: userreal4 = 0 72: applied-forces: 72: electric-field: 72: x: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: y: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: z: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: density-guided-simulation: 72: active = false 72: group = protein 72: similarity-measure = inner-product 72: atom-spreading-weight = unity 72: force-constant = 1e+09 72: gaussian-transform-spreading-width = 0.2 72: gaussian-transform-spreading-range-in-multiples-of-width = 4 72: reference-density-filename = reference.mrc 72: nst = 1 72: normalize-densities = true 72: adaptive-force-scaling = false 72: adaptive-force-scaling-time-constant = 4 72: shift-vector = 72: transformation-matrix = 72: qmmm-cp2k: 72: active = false 72: qmgroup = System 72: qmmethod = PBE 72: qmfilenames = 72: qmcharge = 0 72: qmmultiplicity = 1 72: colvars: 72: active = false 72: configfile = 72: seed = -1 72: nnpot: 72: active = false 72: modelfile = model.pt 72: input-group = System 72: link-type = H 72: link-distance = 0.1 72: pair-cutoff = 0 72: embedding = mechanical 72: nnp-charge = 0 72: model-input1 = 72: model-input2 = 72: model-input3 = 72: model-input4 = 72: model-input5 = 72: model-input6 = 72: model-input7 = 72: model-input8 = 72: model-input9 = 72: fast-multipole-method: 72: fmm: 72: backend = inactive 72: exafmm-order = 6 72: exafmm-direct-range = 2 72: exafmm-direct-provider = GROMACS 72: exafmm-tree-type = uniform 72: exafmm-tree-depth = 0 72: exafmm-max-particles-per-cell = 0 72: fmsolvr-order = 8 72: fmsolvr-direct-range = 1 72: fmsolvr-direct-provider = FMM 72: fmsolvr-dipole-compensation = true 72: fmsolvr-tree-depth = 3 72: fmsolvr-sparse = false 72: grpopts: 72: nrdf: 465 72: ref-t: 0 72: tau-t: 0 72: annealing: No 72: annealing-npoints: 0 72: acc: 0 0 0 72: nfreeze: N N N 72: energygrp-flags[ 0]: 0 72: header: 72: bIr = present 72: bBox = present 72: bTop = present 72: bX = present 72: bV = present 72: bF = not present 72: natoms = 156 72: lambda = 0.000000e+00 72: buffer size = 57866 72: topology: 72: name="First 10 residues from 1AKI" 72: #atoms = 156 72: #molblock = 1 72: molblock (0): 72: moltype = 0 "Protein_chain_B" 72: #molecules = 1 72: #posres_xA = 0 72: #posres_xB = 0 72: bIntermolecularInteractions = false 72: ffparams: 72: atnr=10 72: ntypes=212 72: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 72: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 72: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 72: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 72: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 72: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 72: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 72: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 72: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 72: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 72: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 72: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 72: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 72: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 72: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 72: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 72: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 72: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 72: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 72: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 72: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 72: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 72: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 72: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 72: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 72: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 72: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 72: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 72: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 72: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 72: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 72: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 72: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 72: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 72: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 72: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 72: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 72: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 72: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 72: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 72: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 72: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 72: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 72: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 72: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 72: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 72: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 72: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 72: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 72: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 72: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 72: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 72: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 72: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 72: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 72: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 72: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 72: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 72: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 72: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 72: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 72: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 72: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 72: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 72: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 72: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 72: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 72: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 72: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 72: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 72: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 72: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 72: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 72: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 72: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 72: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 72: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 72: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 72: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 72: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 72: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 72: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 72: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 72: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 72: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 72: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 72: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 72: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 72: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 72: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 72: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 72: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 72: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 72: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 72: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 72: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 72: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 72: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 72: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 72: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 72: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 72: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 72: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 72: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 72: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 72: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 72: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 72: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 72: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 72: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 72: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 72: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 72: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 72: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 72: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 72: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 72: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 72: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 72: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 72: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 72: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 72: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 72: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 72: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 72: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 72: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 72: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 72: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 72: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 72: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 72: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 72: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 72: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 72: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 72: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 72: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 72: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 72: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 72: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 72: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 72: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 72: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 72: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 72: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 72: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 72: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 72: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 72: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 72: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 72: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 72: reppow = 12 72: fudgeQQ = 0.5 72: cmap 72: moltype (0): 72: name="Protein_chain_B" 72: atoms: 72: atom (156): 72: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 72: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 72: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 72: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 72: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 72: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 72: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 72: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 72: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 72: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 72: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 72: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 72: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 72: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 72: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 72: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 72: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 72: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 72: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 72: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 72: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 72: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 72: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 72: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 72: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 72: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 72: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 72: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 72: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 72: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 72: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 72: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 72: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 72: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 72: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 72: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 72: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 72: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 72: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 72: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 72: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 72: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 72: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 72: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 72: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 72: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 72: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 72: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 72: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 72: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 72: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 72: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 72: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 72: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 72: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 72: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 72: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 72: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 72: atom (156): 72: atom[0]={name="N"} 72: atom[1]={name="H1"} 72: atom[2]={name="H2"} 72: atom[3]={name="H3"} 72: atom[4]={name="CA"} 72: atom[5]={name="HA"} 72: atom[6]={name="CB"} 72: atom[7]={name="HB1"} 72: atom[8]={name="HB2"} 72: atom[9]={name="CG"} 72: atom[10]={name="HG1"} 72: atom[11]={name="HG2"} 72: atom[12]={name="CD"} 72: atom[13]={name="HD1"} 72: atom[14]={name="HD2"} 72: atom[15]={name="CE"} 72: atom[16]={name="HE1"} 72: atom[17]={name="HE2"} 72: atom[18]={name="NZ"} 72: atom[19]={name="HZ1"} 72: atom[20]={name="HZ2"} 72: atom[21]={name="HZ3"} 72: atom[22]={name="C"} 72: atom[23]={name="O"} 72: atom[24]={name="N"} 72: atom[25]={name="H"} 72: atom[26]={name="CA"} 72: atom[27]={name="HA"} 72: atom[28]={name="CB"} 72: atom[29]={name="HB"} 72: atom[30]={name="CG1"} 72: atom[31]={name="HG11"} 72: atom[32]={name="HG12"} 72: atom[33]={name="HG13"} 72: atom[34]={name="CG2"} 72: atom[35]={name="HG21"} 72: atom[36]={name="HG22"} 72: atom[37]={name="HG23"} 72: atom[38]={name="C"} 72: atom[39]={name="O"} 72: atom[40]={name="N"} 72: atom[41]={name="H"} 72: atom[42]={name="CA"} 72: atom[43]={name="HA"} 72: atom[44]={name="CB"} 72: atom[45]={name="HB1"} 72: atom[46]={name="HB2"} 72: atom[47]={name="CG"} 72: atom[48]={name="CD1"} 72: atom[49]={name="HD1"} 72: atom[50]={name="CD2"} 72: atom[51]={name="HD2"} 72: atom[52]={name="CE1"} 72: atom[53]={name="HE1"} 72: atom[54]={name="CE2"} 72: atom[55]={name="HE2"} 72: atom[56]={name="CZ"} 72: atom[57]={name="HZ"} 72: atom[58]={name="C"} 72: atom[59]={name="O"} 72: atom[60]={name="N"} 72: atom[61]={name="H"} 72: atom[62]={name="CA"} 72: atom[63]={name="HA1"} 72: atom[64]={name="HA2"} 72: atom[65]={name="C"} 72: atom[66]={name="O"} 72: atom[67]={name="N"} 72: atom[68]={name="H"} 72: atom[69]={name="CA"} 72: atom[70]={name="HA"} 72: atom[71]={name="CB"} 72: atom[72]={name="HB1"} 72: atom[73]={name="HB2"} 72: atom[74]={name="CG"} 72: atom[75]={name="HG1"} 72: atom[76]={name="HG2"} 72: atom[77]={name="CD"} 72: atom[78]={name="HD1"} 72: atom[79]={name="HD2"} 72: atom[80]={name="NE"} 72: atom[81]={name="HE"} 72: atom[82]={name="CZ"} 72: atom[83]={name="NH1"} 72: atom[84]={name="HH11"} 72: atom[85]={name="HH12"} 72: atom[86]={name="NH2"} 72: atom[87]={name="HH21"} 72: atom[88]={name="HH22"} 72: atom[89]={name="C"} 72: atom[90]={name="O"} 72: atom[91]={name="N"} 72: atom[92]={name="H"} 72: atom[93]={name="CA"} 72: atom[94]={name="HA"} 72: atom[95]={name="CB"} 72: atom[96]={name="HB1"} 72: atom[97]={name="HB2"} 72: atom[98]={name="SG"} 72: atom[99]={name="HG"} 72: atom[100]={name="C"} 72: atom[101]={name="O"} 72: atom[102]={name="N"} 72: atom[103]={name="H"} 72: atom[104]={name="CA"} 72: atom[105]={name="HA"} 72: atom[106]={name="CB"} 72: atom[107]={name="HB1"} 72: atom[108]={name="HB2"} 72: atom[109]={name="CG"} 72: atom[110]={name="HG1"} 72: atom[111]={name="HG2"} 72: atom[112]={name="CD"} 72: atom[113]={name="OE1"} 72: atom[114]={name="OE2"} 72: atom[115]={name="C"} 72: atom[116]={name="O"} 72: atom[117]={name="N"} 72: atom[118]={name="H"} 72: atom[119]={name="CA"} 72: atom[120]={name="HA"} 72: atom[121]={name="CB"} 72: atom[122]={name="HB1"} 72: atom[123]={name="HB2"} 72: atom[124]={name="CG"} 72: atom[125]={name="HG"} 72: atom[126]={name="CD1"} 72: atom[127]={name="HD11"} 72: atom[128]={name="HD12"} 72: atom[129]={name="HD13"} 72: atom[130]={name="CD2"} 72: atom[131]={name="HD21"} 72: atom[132]={name="HD22"} 72: atom[133]={name="HD23"} 72: atom[134]={name="C"} 72: atom[135]={name="O"} 72: atom[136]={name="N"} 72: atom[137]={name="H"} 72: atom[138]={name="CA"} 72: atom[139]={name="HA"} 72: atom[140]={name="CB"} 72: atom[141]={name="HB1"} 72: atom[142]={name="HB2"} 72: atom[143]={name="HB3"} 72: atom[144]={name="C"} 72: atom[145]={name="O"} 72: atom[146]={name="N"} 72: atom[147]={name="H"} 72: atom[148]={name="CA"} 72: atom[149]={name="HA"} 72: atom[150]={name="CB"} 72: atom[151]={name="HB1"} 72: atom[152]={name="HB2"} 72: atom[153]={name="HB3"} 72: atom[154]={name="C"} 72: atom[155]={name="O"} 72: type (156): 72: type[0]={name="opls_287",nameB="opls_287"} 72: type[1]={name="opls_290",nameB="opls_290"} 72: type[2]={name="opls_290",nameB="opls_290"} 72: type[3]={name="opls_290",nameB="opls_290"} 72: type[4]={name="opls_293B",nameB="opls_293B"} 72: type[5]={name="opls_140",nameB="opls_140"} 72: type[6]={name="opls_136",nameB="opls_136"} 72: type[7]={name="opls_140",nameB="opls_140"} 72: type[8]={name="opls_140",nameB="opls_140"} 72: type[9]={name="opls_136",nameB="opls_136"} 72: type[10]={name="opls_140",nameB="opls_140"} 72: type[11]={name="opls_140",nameB="opls_140"} 72: type[12]={name="opls_136",nameB="opls_136"} 72: type[13]={name="opls_140",nameB="opls_140"} 72: type[14]={name="opls_140",nameB="opls_140"} 72: type[15]={name="opls_292",nameB="opls_292"} 72: type[16]={name="opls_140",nameB="opls_140"} 72: type[17]={name="opls_140",nameB="opls_140"} 72: type[18]={name="opls_287",nameB="opls_287"} 72: type[19]={name="opls_290",nameB="opls_290"} 72: type[20]={name="opls_290",nameB="opls_290"} 72: type[21]={name="opls_290",nameB="opls_290"} 72: type[22]={name="opls_235",nameB="opls_235"} 72: type[23]={name="opls_236",nameB="opls_236"} 72: type[24]={name="opls_238",nameB="opls_238"} 72: type[25]={name="opls_241",nameB="opls_241"} 72: type[26]={name="opls_224B",nameB="opls_224B"} 72: type[27]={name="opls_140",nameB="opls_140"} 72: type[28]={name="opls_137",nameB="opls_137"} 72: type[29]={name="opls_140",nameB="opls_140"} 72: type[30]={name="opls_135",nameB="opls_135"} 72: type[31]={name="opls_140",nameB="opls_140"} 72: type[32]={name="opls_140",nameB="opls_140"} 72: type[33]={name="opls_140",nameB="opls_140"} 72: type[34]={name="opls_135",nameB="opls_135"} 72: type[35]={name="opls_140",nameB="opls_140"} 72: type[36]={name="opls_140",nameB="opls_140"} 72: type[37]={name="opls_140",nameB="opls_140"} 72: type[38]={name="opls_235",nameB="opls_235"} 72: type[39]={name="opls_236",nameB="opls_236"} 72: type[40]={name="opls_238",nameB="opls_238"} 72: type[41]={name="opls_241",nameB="opls_241"} 72: type[42]={name="opls_224B",nameB="opls_224B"} 72: type[43]={name="opls_140",nameB="opls_140"} 72: type[44]={name="opls_149",nameB="opls_149"} 72: type[45]={name="opls_140",nameB="opls_140"} 72: type[46]={name="opls_140",nameB="opls_140"} 72: type[47]={name="opls_145",nameB="opls_145"} 72: type[48]={name="opls_145",nameB="opls_145"} 72: type[49]={name="opls_146",nameB="opls_146"} 72: type[50]={name="opls_145",nameB="opls_145"} 72: type[51]={name="opls_146",nameB="opls_146"} 72: type[52]={name="opls_145",nameB="opls_145"} 72: type[53]={name="opls_146",nameB="opls_146"} 72: type[54]={name="opls_145",nameB="opls_145"} 72: type[55]={name="opls_146",nameB="opls_146"} 72: type[56]={name="opls_145",nameB="opls_145"} 72: type[57]={name="opls_146",nameB="opls_146"} 72: type[58]={name="opls_235",nameB="opls_235"} 72: type[59]={name="opls_236",nameB="opls_236"} 72: type[60]={name="opls_238",nameB="opls_238"} 72: type[61]={name="opls_241",nameB="opls_241"} 72: type[62]={name="opls_223B",nameB="opls_223B"} 72: type[63]={name="opls_140",nameB="opls_140"} 72: type[64]={name="opls_140",nameB="opls_140"} 72: type[65]={name="opls_235",nameB="opls_235"} 72: type[66]={name="opls_236",nameB="opls_236"} 72: type[67]={name="opls_238",nameB="opls_238"} 72: type[68]={name="opls_241",nameB="opls_241"} 72: type[69]={name="opls_224B",nameB="opls_224B"} 72: type[70]={name="opls_140",nameB="opls_140"} 72: type[71]={name="opls_136",nameB="opls_136"} 72: type[72]={name="opls_140",nameB="opls_140"} 72: type[73]={name="opls_140",nameB="opls_140"} 72: type[74]={name="opls_308",nameB="opls_308"} 72: type[75]={name="opls_140",nameB="opls_140"} 72: type[76]={name="opls_140",nameB="opls_140"} 72: type[77]={name="opls_307",nameB="opls_307"} 72: type[78]={name="opls_140",nameB="opls_140"} 72: type[79]={name="opls_140",nameB="opls_140"} 72: type[80]={name="opls_303",nameB="opls_303"} 72: type[81]={name="opls_304",nameB="opls_304"} 72: type[82]={name="opls_302",nameB="opls_302"} 72: type[83]={name="opls_300",nameB="opls_300"} 72: type[84]={name="opls_301",nameB="opls_301"} 72: type[85]={name="opls_301",nameB="opls_301"} 72: type[86]={name="opls_300",nameB="opls_300"} 72: type[87]={name="opls_301",nameB="opls_301"} 72: type[88]={name="opls_301",nameB="opls_301"} 72: type[89]={name="opls_235",nameB="opls_235"} 72: type[90]={name="opls_236",nameB="opls_236"} 72: type[91]={name="opls_238",nameB="opls_238"} 72: type[92]={name="opls_241",nameB="opls_241"} 72: type[93]={name="opls_224B",nameB="opls_224B"} 72: type[94]={name="opls_140",nameB="opls_140"} 72: type[95]={name="opls_206",nameB="opls_206"} 72: type[96]={name="opls_140",nameB="opls_140"} 72: type[97]={name="opls_140",nameB="opls_140"} 72: type[98]={name="opls_200",nameB="opls_200"} 72: type[99]={name="opls_204",nameB="opls_204"} 72: type[100]={name="opls_235",nameB="opls_235"} 72: type[101]={name="opls_236",nameB="opls_236"} 72: type[102]={name="opls_238",nameB="opls_238"} 72: type[103]={name="opls_241",nameB="opls_241"} 72: type[104]={name="opls_224B",nameB="opls_224B"} 72: type[105]={name="opls_140",nameB="opls_140"} 72: type[106]={name="opls_136",nameB="opls_136"} 72: type[107]={name="opls_140",nameB="opls_140"} 72: type[108]={name="opls_140",nameB="opls_140"} 72: type[109]={name="opls_274",nameB="opls_274"} 72: type[110]={name="opls_140",nameB="opls_140"} 72: type[111]={name="opls_140",nameB="opls_140"} 72: type[112]={name="opls_271",nameB="opls_271"} 72: type[113]={name="opls_272",nameB="opls_272"} 72: type[114]={name="opls_272",nameB="opls_272"} 72: type[115]={name="opls_235",nameB="opls_235"} 72: type[116]={name="opls_236",nameB="opls_236"} 72: type[117]={name="opls_238",nameB="opls_238"} 72: type[118]={name="opls_241",nameB="opls_241"} 72: type[119]={name="opls_224B",nameB="opls_224B"} 72: type[120]={name="opls_140",nameB="opls_140"} 72: type[121]={name="opls_136",nameB="opls_136"} 72: type[122]={name="opls_140",nameB="opls_140"} 72: type[123]={name="opls_140",nameB="opls_140"} 72: type[124]={name="opls_137",nameB="opls_137"} 72: type[125]={name="opls_140",nameB="opls_140"} 72: type[126]={name="opls_135",nameB="opls_135"} 72: type[127]={name="opls_140",nameB="opls_140"} 72: type[128]={name="opls_140",nameB="opls_140"} 72: type[129]={name="opls_140",nameB="opls_140"} 72: type[130]={name="opls_135",nameB="opls_135"} 72: type[131]={name="opls_140",nameB="opls_140"} 72: type[132]={name="opls_140",nameB="opls_140"} 72: type[133]={name="opls_140",nameB="opls_140"} 72: type[134]={name="opls_235",nameB="opls_235"} 72: type[135]={name="opls_236",nameB="opls_236"} 72: type[136]={name="opls_238",nameB="opls_238"} 72: type[137]={name="opls_241",nameB="opls_241"} 72: type[138]={name="opls_224B",nameB="opls_224B"} 72: type[139]={name="opls_140",nameB="opls_140"} 72: type[140]={name="opls_135",nameB="opls_135"} 72: type[141]={name="opls_140",nameB="opls_140"} 72: type[142]={name="opls_140",nameB="opls_140"} 72: type[143]={name="opls_140",nameB="opls_140"} 72: type[144]={name="opls_235",nameB="opls_235"} 72: type[145]={name="opls_236",nameB="opls_236"} 72: type[146]={name="opls_238",nameB="opls_238"} 72: type[147]={name="opls_241",nameB="opls_241"} 72: type[148]={name="opls_224B",nameB="opls_224B"} 72: type[149]={name="opls_140",nameB="opls_140"} 72: type[150]={name="opls_135",nameB="opls_135"} 72: type[151]={name="opls_140",nameB="opls_140"} 72: type[152]={name="opls_140",nameB="opls_140"} 72: type[153]={name="opls_140",nameB="opls_140"} 72: type[154]={name="opls_235",nameB="opls_235"} 72: type[155]={name="opls_236",nameB="opls_236"} 72: residue (10): 72: residue[0]={name="LYS", nr=1, ic=' '} 72: residue[1]={name="VAL", nr=2, ic=' '} 72: residue[2]={name="PHE", nr=3, ic=' '} 72: residue[3]={name="GLY", nr=4, ic=' '} 72: residue[4]={name="ARG", nr=5, ic=' '} 72: residue[5]={name="CYS", nr=6, ic=' '} 72: residue[6]={name="GLU", nr=7, ic=' '} 72: residue[7]={name="LEU", nr=8, ic=' '} 72: residue[8]={name="ALA", nr=9, ic=' '} 72: residue[9]={name="ALA", nr=10, ic=' '} 72: excls: 72: numLists=156 72: numElements=1828 72: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 72: 23, 24, 25, 26} 72: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 72: 14, 15, 22, 23, 24} 72: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 72: 16, 17, 18, 22} 72: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 72: 17, 18, 19, 20, 21} 72: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 72: 20, 21} 72: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 72: 26, 27, 28, 38} 72: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 72: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 72: 30, 34, 38, 39, 40} 72: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 72: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 72: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 72: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40} 72: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 72: 34, 35, 36, 37, 38, 39, 40} 72: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40, 41, 42, 43, 44, 58} 72: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 72: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 72: 45, 46, 47, 58, 59, 60} 72: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 72: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 72: 48, 50, 58, 59, 60, 61, 62} 72: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60} 72: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 72: 50, 51, 52, 54, 58, 59, 60} 72: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 72: 52, 53, 54, 55, 56, 58} 72: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 72: 54, 56, 57} 72: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 72: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 72: 55, 56, 57} 72: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 72: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 72: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 72: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 72: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 72: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60, 61, 62, 63, 64, 65} 72: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 72: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 72: 65, 66, 67} 72: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 72: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 72: 68, 69} 72: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72: 70, 71, 89} 72: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 72: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72: 72, 73, 74, 89, 90, 91} 72: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 72: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 72: 75, 76, 77, 89, 90, 91, 92, 93} 72: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91} 72: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 72: 77, 78, 79, 80, 89, 90, 91} 72: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 72: 79, 80, 81, 82, 89} 72: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 72: 81, 82, 83, 86} 72: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 72: 84, 85, 86, 87, 88} 72: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 72: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 72: 87, 88} 72: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[84][num=6]={80, 82, 83, 84, 85, 86} 72: excls[85][num=6]={80, 82, 83, 84, 85, 86} 72: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[87][num=6]={80, 82, 83, 86, 87, 88} 72: excls[88][num=6]={80, 82, 83, 86, 87, 88} 72: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91, 92, 93, 94, 95, 100} 72: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 72: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 72: 96, 97, 98, 100, 101, 102} 72: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 72: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 72: 99, 100, 101, 102, 103, 104} 72: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102} 72: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 72: 101, 102} 72: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[99][num=6]={93, 95, 96, 97, 98, 99} 72: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102, 103, 104, 105, 106, 115} 72: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 72: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 72: 106, 107, 108, 109, 115, 116, 117} 72: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 72: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 72: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 72: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117} 72: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 110, 111, 112, 113, 114, 115, 116, 117} 72: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 113, 114, 115} 72: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 72: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 72: 120, 121, 122, 123, 124, 134, 135, 136} 72: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 72: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 72: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136} 72: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 72: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 127, 128, 129, 130, 131, 132, 133, 134} 72: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 72: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 72: 139, 140, 141, 142, 143, 144, 145, 146} 72: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 72: 142, 143, 144, 145, 146, 147, 148} 72: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 72: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 72: 149, 150, 151, 152, 153, 154, 155} 72: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 72: 152, 153, 154, 155} 72: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[155][num=6]={146, 148, 149, 150, 154, 155} 72: Bond: 72: nr: 468 72: iatoms: 72: 0 type=100 (BONDS) 0 1 72: 1 type=100 (BONDS) 0 2 72: 2 type=100 (BONDS) 0 3 72: 3 type=101 (BONDS) 0 4 72: 4 type=102 (BONDS) 4 5 72: 5 type=103 (BONDS) 4 6 72: 6 type=104 (BONDS) 4 22 72: 7 type=102 (BONDS) 6 7 72: 8 type=102 (BONDS) 6 8 72: 9 type=103 (BONDS) 6 9 72: 10 type=102 (BONDS) 9 10 72: 11 type=102 (BONDS) 9 11 72: 12 type=103 (BONDS) 9 12 72: 13 type=102 (BONDS) 12 13 72: 14 type=102 (BONDS) 12 14 72: 15 type=103 (BONDS) 12 15 72: 16 type=102 (BONDS) 15 16 72: 17 type=102 (BONDS) 15 17 72: 18 type=101 (BONDS) 15 18 72: 19 type=100 (BONDS) 18 19 72: 20 type=100 (BONDS) 18 20 72: 21 type=100 (BONDS) 18 21 72: 22 type=105 (BONDS) 22 23 72: 23 type=106 (BONDS) 22 24 72: 24 type=100 (BONDS) 24 25 72: 25 type=107 (BONDS) 24 26 72: 26 type=102 (BONDS) 26 27 72: 27 type=103 (BONDS) 26 28 72: 28 type=104 (BONDS) 26 38 72: 29 type=102 (BONDS) 28 29 72: 30 type=103 (BONDS) 28 30 72: 31 type=103 (BONDS) 28 34 72: 32 type=102 (BONDS) 30 31 72: 33 type=102 (BONDS) 30 32 72: 34 type=102 (BONDS) 30 33 72: 35 type=102 (BONDS) 34 35 72: 36 type=102 (BONDS) 34 36 72: 37 type=102 (BONDS) 34 37 72: 38 type=105 (BONDS) 38 39 72: 39 type=106 (BONDS) 38 40 72: 40 type=100 (BONDS) 40 41 72: 41 type=107 (BONDS) 40 42 72: 42 type=102 (BONDS) 42 43 72: 43 type=103 (BONDS) 42 44 72: 44 type=104 (BONDS) 42 58 72: 45 type=102 (BONDS) 44 45 72: 46 type=102 (BONDS) 44 46 72: 47 type=108 (BONDS) 44 47 72: 48 type=109 (BONDS) 47 48 72: 49 type=109 (BONDS) 47 50 72: 50 type=110 (BONDS) 48 49 72: 51 type=109 (BONDS) 48 52 72: 52 type=110 (BONDS) 50 51 72: 53 type=109 (BONDS) 50 54 72: 54 type=110 (BONDS) 52 53 72: 55 type=109 (BONDS) 52 56 72: 56 type=110 (BONDS) 54 55 72: 57 type=109 (BONDS) 54 56 72: 58 type=110 (BONDS) 56 57 72: 59 type=105 (BONDS) 58 59 72: 60 type=106 (BONDS) 58 60 72: 61 type=100 (BONDS) 60 61 72: 62 type=107 (BONDS) 60 62 72: 63 type=102 (BONDS) 62 63 72: 64 type=102 (BONDS) 62 64 72: 65 type=104 (BONDS) 62 65 72: 66 type=105 (BONDS) 65 66 72: 67 type=106 (BONDS) 65 67 72: 68 type=100 (BONDS) 67 68 72: 69 type=107 (BONDS) 67 69 72: 70 type=102 (BONDS) 69 70 72: 71 type=103 (BONDS) 69 71 72: 72 type=104 (BONDS) 69 89 72: 73 type=102 (BONDS) 71 72 72: 74 type=102 (BONDS) 71 73 72: 75 type=103 (BONDS) 71 74 72: 76 type=102 (BONDS) 74 75 72: 77 type=102 (BONDS) 74 76 72: 78 type=103 (BONDS) 74 77 72: 79 type=102 (BONDS) 77 78 72: 80 type=102 (BONDS) 77 79 72: 81 type=111 (BONDS) 77 80 72: 82 type=100 (BONDS) 80 81 72: 83 type=112 (BONDS) 80 82 72: 84 type=112 (BONDS) 82 83 72: 85 type=112 (BONDS) 82 86 72: 86 type=100 (BONDS) 83 84 72: 87 type=100 (BONDS) 83 85 72: 88 type=100 (BONDS) 86 87 72: 89 type=100 (BONDS) 86 88 72: 90 type=105 (BONDS) 89 90 72: 91 type=106 (BONDS) 89 91 72: 92 type=100 (BONDS) 91 92 72: 93 type=107 (BONDS) 91 93 72: 94 type=102 (BONDS) 93 94 72: 95 type=103 (BONDS) 93 95 72: 96 type=104 (BONDS) 93 100 72: 97 type=102 (BONDS) 95 96 72: 98 type=102 (BONDS) 95 97 72: 99 type=113 (BONDS) 95 98 72: 100 type=114 (BONDS) 98 99 72: 101 type=105 (BONDS) 100 101 72: 102 type=106 (BONDS) 100 102 72: 103 type=100 (BONDS) 102 103 72: 104 type=107 (BONDS) 102 104 72: 105 type=102 (BONDS) 104 105 72: 106 type=103 (BONDS) 104 106 72: 107 type=104 (BONDS) 104 115 72: 108 type=102 (BONDS) 106 107 72: 109 type=102 (BONDS) 106 108 72: 110 type=103 (BONDS) 106 109 72: 111 type=102 (BONDS) 109 110 72: 112 type=102 (BONDS) 109 111 72: 113 type=104 (BONDS) 109 112 72: 114 type=115 (BONDS) 112 113 72: 115 type=115 (BONDS) 112 114 72: 116 type=105 (BONDS) 115 116 72: 117 type=106 (BONDS) 115 117 72: 118 type=100 (BONDS) 117 118 72: 119 type=107 (BONDS) 117 119 72: 120 type=102 (BONDS) 119 120 72: 121 type=103 (BONDS) 119 121 72: 122 type=104 (BONDS) 119 134 72: 123 type=102 (BONDS) 121 122 72: 124 type=102 (BONDS) 121 123 72: 125 type=103 (BONDS) 121 124 72: 126 type=102 (BONDS) 124 125 72: 127 type=103 (BONDS) 124 126 72: 128 type=103 (BONDS) 124 130 72: 129 type=102 (BONDS) 126 127 72: 130 type=102 (BONDS) 126 128 72: 131 type=102 (BONDS) 126 129 72: 132 type=102 (BONDS) 130 131 72: 133 type=102 (BONDS) 130 132 72: 134 type=102 (BONDS) 130 133 72: 135 type=105 (BONDS) 134 135 72: 136 type=106 (BONDS) 134 136 72: 137 type=100 (BONDS) 136 137 72: 138 type=107 (BONDS) 136 138 72: 139 type=102 (BONDS) 138 139 72: 140 type=103 (BONDS) 138 140 72: 141 type=104 (BONDS) 138 144 72: 142 type=102 (BONDS) 140 141 72: 143 type=102 (BONDS) 140 142 72: 144 type=102 (BONDS) 140 143 72: 145 type=105 (BONDS) 144 145 72: 146 type=106 (BONDS) 144 146 72: 147 type=100 (BONDS) 146 147 72: 148 type=107 (BONDS) 146 148 72: 149 type=102 (BONDS) 148 149 72: 150 type=103 (BONDS) 148 150 72: 151 type=104 (BONDS) 148 154 72: 152 type=102 (BONDS) 150 151 72: 153 type=102 (BONDS) 150 152 72: 154 type=102 (BONDS) 150 153 72: 155 type=105 (BONDS) 154 155 72: G96Bond: 72: nr: 0 72: Morse: 72: nr: 0 72: Cubic Bonds: 72: nr: 0 72: Connect Bonds: 72: nr: 0 72: Harmonic Pot.: 72: nr: 0 72: FENE Bonds: 72: nr: 0 72: Tab. Bonds: 72: nr: 0 72: Tab. Bonds NC: 72: nr: 0 72: Restraint Pot.: 72: nr: 0 72: Angle: 72: nr: 1124 72: iatoms: 72: 0 type=116 (ANGLES) 1 0 2 72: 1 type=116 (ANGLES) 1 0 3 72: 2 type=116 (ANGLES) 1 0 4 72: 3 type=116 (ANGLES) 2 0 3 72: 4 type=116 (ANGLES) 2 0 4 72: 5 type=116 (ANGLES) 3 0 4 72: 6 type=116 (ANGLES) 0 4 5 72: 7 type=117 (ANGLES) 0 4 6 72: 8 type=117 (ANGLES) 0 4 22 72: 9 type=118 (ANGLES) 5 4 6 72: 10 type=116 (ANGLES) 5 4 22 72: 11 type=119 (ANGLES) 6 4 22 72: 12 type=118 (ANGLES) 4 6 7 72: 13 type=118 (ANGLES) 4 6 8 72: 14 type=120 (ANGLES) 4 6 9 72: 15 type=121 (ANGLES) 7 6 8 72: 16 type=118 (ANGLES) 7 6 9 72: 17 type=118 (ANGLES) 8 6 9 72: 18 type=118 (ANGLES) 6 9 10 72: 19 type=118 (ANGLES) 6 9 11 72: 20 type=120 (ANGLES) 6 9 12 72: 21 type=121 (ANGLES) 10 9 11 72: 22 type=118 (ANGLES) 10 9 12 72: 23 type=118 (ANGLES) 11 9 12 72: 24 type=118 (ANGLES) 9 12 13 72: 25 type=118 (ANGLES) 9 12 14 72: 26 type=120 (ANGLES) 9 12 15 72: 27 type=121 (ANGLES) 13 12 14 72: 28 type=118 (ANGLES) 13 12 15 72: 29 type=118 (ANGLES) 14 12 15 72: 30 type=118 (ANGLES) 12 15 16 72: 31 type=118 (ANGLES) 12 15 17 72: 32 type=117 (ANGLES) 12 15 18 72: 33 type=121 (ANGLES) 16 15 17 72: 34 type=116 (ANGLES) 16 15 18 72: 35 type=116 (ANGLES) 17 15 18 72: 36 type=116 (ANGLES) 15 18 19 72: 37 type=116 (ANGLES) 15 18 20 72: 38 type=116 (ANGLES) 15 18 21 72: 39 type=116 (ANGLES) 19 18 20 72: 40 type=116 (ANGLES) 19 18 21 72: 41 type=116 (ANGLES) 20 18 21 72: 42 type=122 (ANGLES) 4 22 23 72: 43 type=123 (ANGLES) 4 22 24 72: 44 type=124 (ANGLES) 23 22 24 72: 45 type=125 (ANGLES) 22 24 25 72: 46 type=126 (ANGLES) 22 24 26 72: 47 type=127 (ANGLES) 25 24 26 72: 48 type=116 (ANGLES) 24 26 27 72: 49 type=128 (ANGLES) 24 26 28 72: 50 type=129 (ANGLES) 24 26 38 72: 51 type=118 (ANGLES) 27 26 28 72: 52 type=116 (ANGLES) 27 26 38 72: 53 type=119 (ANGLES) 28 26 38 72: 54 type=118 (ANGLES) 26 28 29 72: 55 type=120 (ANGLES) 26 28 30 72: 56 type=120 (ANGLES) 26 28 34 72: 57 type=118 (ANGLES) 29 28 30 72: 58 type=118 (ANGLES) 29 28 34 72: 59 type=120 (ANGLES) 30 28 34 72: 60 type=118 (ANGLES) 28 30 31 72: 61 type=118 (ANGLES) 28 30 32 72: 62 type=118 (ANGLES) 28 30 33 72: 63 type=121 (ANGLES) 31 30 32 72: 64 type=121 (ANGLES) 31 30 33 72: 65 type=121 (ANGLES) 32 30 33 72: 66 type=118 (ANGLES) 28 34 35 72: 67 type=118 (ANGLES) 28 34 36 72: 68 type=118 (ANGLES) 28 34 37 72: 69 type=121 (ANGLES) 35 34 36 72: 70 type=121 (ANGLES) 35 34 37 72: 71 type=121 (ANGLES) 36 34 37 72: 72 type=122 (ANGLES) 26 38 39 72: 73 type=123 (ANGLES) 26 38 40 72: 74 type=124 (ANGLES) 39 38 40 72: 75 type=125 (ANGLES) 38 40 41 72: 76 type=126 (ANGLES) 38 40 42 72: 77 type=127 (ANGLES) 41 40 42 72: 78 type=116 (ANGLES) 40 42 43 72: 79 type=128 (ANGLES) 40 42 44 72: 80 type=129 (ANGLES) 40 42 58 72: 81 type=118 (ANGLES) 43 42 44 72: 82 type=116 (ANGLES) 43 42 58 72: 83 type=119 (ANGLES) 44 42 58 72: 84 type=118 (ANGLES) 42 44 45 72: 85 type=118 (ANGLES) 42 44 46 72: 86 type=130 (ANGLES) 42 44 47 72: 87 type=121 (ANGLES) 45 44 46 72: 88 type=116 (ANGLES) 45 44 47 72: 89 type=116 (ANGLES) 46 44 47 72: 90 type=131 (ANGLES) 44 47 48 72: 91 type=131 (ANGLES) 44 47 50 72: 92 type=132 (ANGLES) 48 47 50 72: 93 type=133 (ANGLES) 47 48 49 72: 94 type=132 (ANGLES) 47 48 52 72: 95 type=133 (ANGLES) 49 48 52 72: 96 type=133 (ANGLES) 47 50 51 72: 97 type=132 (ANGLES) 47 50 54 72: 98 type=133 (ANGLES) 51 50 54 72: 99 type=133 (ANGLES) 48 52 53 72: 100 type=132 (ANGLES) 48 52 56 72: 101 type=133 (ANGLES) 53 52 56 72: 102 type=133 (ANGLES) 50 54 55 72: 103 type=132 (ANGLES) 50 54 56 72: 104 type=133 (ANGLES) 55 54 56 72: 105 type=132 (ANGLES) 52 56 54 72: 106 type=133 (ANGLES) 52 56 57 72: 107 type=133 (ANGLES) 54 56 57 72: 108 type=122 (ANGLES) 42 58 59 72: 109 type=123 (ANGLES) 42 58 60 72: 110 type=124 (ANGLES) 59 58 60 72: 111 type=125 (ANGLES) 58 60 61 72: 112 type=126 (ANGLES) 58 60 62 72: 113 type=127 (ANGLES) 61 60 62 72: 114 type=116 (ANGLES) 60 62 63 72: 115 type=116 (ANGLES) 60 62 64 72: 116 type=129 (ANGLES) 60 62 65 72: 117 type=121 (ANGLES) 63 62 64 72: 118 type=116 (ANGLES) 63 62 65 72: 119 type=116 (ANGLES) 64 62 65 72: 120 type=122 (ANGLES) 62 65 66 72: 121 type=123 (ANGLES) 62 65 67 72: 122 type=124 (ANGLES) 66 65 67 72: 123 type=125 (ANGLES) 65 67 68 72: 124 type=126 (ANGLES) 65 67 69 72: 125 type=127 (ANGLES) 68 67 69 72: 126 type=116 (ANGLES) 67 69 70 72: 127 type=128 (ANGLES) 67 69 71 72: 128 type=129 (ANGLES) 67 69 89 72: 129 type=118 (ANGLES) 70 69 71 72: 130 type=116 (ANGLES) 70 69 89 72: 131 type=119 (ANGLES) 71 69 89 72: 132 type=118 (ANGLES) 69 71 72 72: 133 type=118 (ANGLES) 69 71 73 72: 134 type=120 (ANGLES) 69 71 74 72: 135 type=121 (ANGLES) 72 71 73 72: 136 type=118 (ANGLES) 72 71 74 72: 137 type=118 (ANGLES) 73 71 74 72: 138 type=118 (ANGLES) 71 74 75 72: 139 type=118 (ANGLES) 71 74 76 72: 140 type=120 (ANGLES) 71 74 77 72: 141 type=121 (ANGLES) 75 74 76 72: 142 type=118 (ANGLES) 75 74 77 72: 143 type=118 (ANGLES) 76 74 77 72: 144 type=118 (ANGLES) 74 77 78 72: 145 type=118 (ANGLES) 74 77 79 72: 146 type=117 (ANGLES) 74 77 80 72: 147 type=121 (ANGLES) 78 77 79 72: 148 type=116 (ANGLES) 78 77 80 72: 149 type=116 (ANGLES) 79 77 80 72: 150 type=134 (ANGLES) 77 80 81 72: 151 type=135 (ANGLES) 77 80 82 72: 152 type=133 (ANGLES) 81 80 82 72: 153 type=131 (ANGLES) 80 82 83 72: 154 type=131 (ANGLES) 80 82 86 72: 155 type=131 (ANGLES) 83 82 86 72: 156 type=133 (ANGLES) 82 83 84 72: 157 type=133 (ANGLES) 82 83 85 72: 158 type=133 (ANGLES) 84 83 85 72: 159 type=133 (ANGLES) 82 86 87 72: 160 type=133 (ANGLES) 82 86 88 72: 161 type=133 (ANGLES) 87 86 88 72: 162 type=122 (ANGLES) 69 89 90 72: 163 type=123 (ANGLES) 69 89 91 72: 164 type=124 (ANGLES) 90 89 91 72: 165 type=125 (ANGLES) 89 91 92 72: 166 type=126 (ANGLES) 89 91 93 72: 167 type=127 (ANGLES) 92 91 93 72: 168 type=116 (ANGLES) 91 93 94 72: 169 type=128 (ANGLES) 91 93 95 72: 170 type=129 (ANGLES) 91 93 100 72: 171 type=118 (ANGLES) 94 93 95 72: 172 type=116 (ANGLES) 94 93 100 72: 173 type=119 (ANGLES) 95 93 100 72: 174 type=118 (ANGLES) 93 95 96 72: 175 type=118 (ANGLES) 93 95 97 72: 176 type=136 (ANGLES) 93 95 98 72: 177 type=121 (ANGLES) 96 95 97 72: 178 type=116 (ANGLES) 96 95 98 72: 179 type=116 (ANGLES) 97 95 98 72: 180 type=137 (ANGLES) 95 98 99 72: 181 type=122 (ANGLES) 93 100 101 72: 182 type=123 (ANGLES) 93 100 102 72: 183 type=124 (ANGLES) 101 100 102 72: 184 type=125 (ANGLES) 100 102 103 72: 185 type=126 (ANGLES) 100 102 104 72: 186 type=127 (ANGLES) 103 102 104 72: 187 type=116 (ANGLES) 102 104 105 72: 188 type=128 (ANGLES) 102 104 106 72: 189 type=129 (ANGLES) 102 104 115 72: 190 type=118 (ANGLES) 105 104 106 72: 191 type=116 (ANGLES) 105 104 115 72: 192 type=119 (ANGLES) 106 104 115 72: 193 type=118 (ANGLES) 104 106 107 72: 194 type=118 (ANGLES) 104 106 108 72: 195 type=120 (ANGLES) 104 106 109 72: 196 type=121 (ANGLES) 107 106 108 72: 197 type=118 (ANGLES) 107 106 109 72: 198 type=118 (ANGLES) 108 106 109 72: 199 type=118 (ANGLES) 106 109 110 72: 200 type=118 (ANGLES) 106 109 111 72: 201 type=119 (ANGLES) 106 109 112 72: 202 type=121 (ANGLES) 110 109 111 72: 203 type=116 (ANGLES) 110 109 112 72: 204 type=116 (ANGLES) 111 109 112 72: 205 type=138 (ANGLES) 109 112 113 72: 206 type=138 (ANGLES) 109 112 114 72: 207 type=139 (ANGLES) 113 112 114 72: 208 type=122 (ANGLES) 104 115 116 72: 209 type=123 (ANGLES) 104 115 117 72: 210 type=124 (ANGLES) 116 115 117 72: 211 type=125 (ANGLES) 115 117 118 72: 212 type=126 (ANGLES) 115 117 119 72: 213 type=127 (ANGLES) 118 117 119 72: 214 type=116 (ANGLES) 117 119 120 72: 215 type=128 (ANGLES) 117 119 121 72: 216 type=129 (ANGLES) 117 119 134 72: 217 type=118 (ANGLES) 120 119 121 72: 218 type=116 (ANGLES) 120 119 134 72: 219 type=119 (ANGLES) 121 119 134 72: 220 type=118 (ANGLES) 119 121 122 72: 221 type=118 (ANGLES) 119 121 123 72: 222 type=120 (ANGLES) 119 121 124 72: 223 type=121 (ANGLES) 122 121 123 72: 224 type=118 (ANGLES) 122 121 124 72: 225 type=118 (ANGLES) 123 121 124 72: 226 type=118 (ANGLES) 121 124 125 72: 227 type=120 (ANGLES) 121 124 126 72: 228 type=120 (ANGLES) 121 124 130 72: 229 type=118 (ANGLES) 125 124 126 72: 230 type=118 (ANGLES) 125 124 130 72: 231 type=120 (ANGLES) 126 124 130 72: 232 type=118 (ANGLES) 124 126 127 72: 233 type=118 (ANGLES) 124 126 128 72: 234 type=118 (ANGLES) 124 126 129 72: 235 type=121 (ANGLES) 127 126 128 72: 236 type=121 (ANGLES) 127 126 129 72: 237 type=121 (ANGLES) 128 126 129 72: 238 type=118 (ANGLES) 124 130 131 72: 239 type=118 (ANGLES) 124 130 132 72: 240 type=118 (ANGLES) 124 130 133 72: 241 type=121 (ANGLES) 131 130 132 72: 242 type=121 (ANGLES) 131 130 133 72: 243 type=121 (ANGLES) 132 130 133 72: 244 type=122 (ANGLES) 119 134 135 72: 245 type=123 (ANGLES) 119 134 136 72: 246 type=124 (ANGLES) 135 134 136 72: 247 type=125 (ANGLES) 134 136 137 72: 248 type=126 (ANGLES) 134 136 138 72: 249 type=127 (ANGLES) 137 136 138 72: 250 type=116 (ANGLES) 136 138 139 72: 251 type=128 (ANGLES) 136 138 140 72: 252 type=129 (ANGLES) 136 138 144 72: 253 type=118 (ANGLES) 139 138 140 72: 254 type=116 (ANGLES) 139 138 144 72: 255 type=119 (ANGLES) 140 138 144 72: 256 type=118 (ANGLES) 138 140 141 72: 257 type=118 (ANGLES) 138 140 142 72: 258 type=118 (ANGLES) 138 140 143 72: 259 type=121 (ANGLES) 141 140 142 72: 260 type=121 (ANGLES) 141 140 143 72: 261 type=121 (ANGLES) 142 140 143 72: 262 type=122 (ANGLES) 138 144 145 72: 263 type=123 (ANGLES) 138 144 146 72: 264 type=124 (ANGLES) 145 144 146 72: 265 type=125 (ANGLES) 144 146 147 72: 266 type=126 (ANGLES) 144 146 148 72: 267 type=127 (ANGLES) 147 146 148 72: 268 type=116 (ANGLES) 146 148 149 72: 269 type=128 (ANGLES) 146 148 150 72: 270 type=129 (ANGLES) 146 148 154 72: 271 type=118 (ANGLES) 149 148 150 72: 272 type=116 (ANGLES) 149 148 154 72: 273 type=119 (ANGLES) 150 148 154 72: 274 type=118 (ANGLES) 148 150 151 72: 275 type=118 (ANGLES) 148 150 152 72: 276 type=118 (ANGLES) 148 150 153 72: 277 type=121 (ANGLES) 151 150 152 72: 278 type=121 (ANGLES) 151 150 153 72: 279 type=121 (ANGLES) 152 150 153 72: 280 type=122 (ANGLES) 148 154 155 72: G96Angle: 72: nr: 0 72: Restr. Angles: 72: nr: 0 72: Lin. Angle: 72: nr: 0 72: Bond-Cross: 72: nr: 0 72: BA-Cross: 72: nr: 0 72: U-B: 72: nr: 0 72: Quartic Angles: 72: nr: 0 72: Tab. Angles: 72: nr: 0 72: Proper Dih.: 72: nr: 145 72: iatoms: 72: 0 type=140 (PDIHS) 4 24 22 23 72: 1 type=141 (PDIHS) 22 26 24 25 72: 2 type=140 (PDIHS) 26 40 38 39 72: 3 type=141 (PDIHS) 38 42 40 41 72: 4 type=140 (PDIHS) 42 60 58 59 72: 5 type=142 (PDIHS) 44 47 50 48 72: 6 type=142 (PDIHS) 47 52 48 49 72: 7 type=142 (PDIHS) 47 54 50 51 72: 8 type=142 (PDIHS) 48 56 52 53 72: 9 type=142 (PDIHS) 50 56 54 55 72: 10 type=142 (PDIHS) 52 54 56 57 72: 11 type=141 (PDIHS) 58 62 60 61 72: 12 type=140 (PDIHS) 62 67 65 66 72: 13 type=141 (PDIHS) 65 69 67 68 72: 14 type=140 (PDIHS) 69 91 89 90 72: 15 type=141 (PDIHS) 77 82 80 81 72: 16 type=140 (PDIHS) 80 83 82 86 72: 17 type=141 (PDIHS) 82 84 83 85 72: 18 type=141 (PDIHS) 82 87 86 88 72: 19 type=141 (PDIHS) 89 93 91 92 72: 20 type=140 (PDIHS) 93 102 100 101 72: 21 type=141 (PDIHS) 100 104 102 103 72: 22 type=140 (PDIHS) 104 117 115 116 72: 23 type=140 (PDIHS) 109 113 112 114 72: 24 type=141 (PDIHS) 115 119 117 118 72: 25 type=140 (PDIHS) 119 136 134 135 72: 26 type=141 (PDIHS) 134 138 136 137 72: 27 type=140 (PDIHS) 138 146 144 145 72: 28 type=141 (PDIHS) 144 148 146 147 72: Ryckaert-Bell.: 72: nr: 1565 72: iatoms: 72: 0 type=143 (RBDIHS) 1 0 4 5 72: 1 type=144 (RBDIHS) 1 0 4 6 72: 2 type=144 (RBDIHS) 1 0 4 22 72: 3 type=143 (RBDIHS) 2 0 4 5 72: 4 type=144 (RBDIHS) 2 0 4 6 72: 5 type=144 (RBDIHS) 2 0 4 22 72: 6 type=143 (RBDIHS) 3 0 4 5 72: 7 type=144 (RBDIHS) 3 0 4 6 72: 8 type=144 (RBDIHS) 3 0 4 22 72: 9 type=145 (RBDIHS) 0 4 6 9 72: 10 type=146 (RBDIHS) 22 4 6 9 72: 11 type=147 (RBDIHS) 0 4 6 7 72: 12 type=147 (RBDIHS) 0 4 6 8 72: 13 type=148 (RBDIHS) 5 4 6 7 72: 14 type=148 (RBDIHS) 5 4 6 8 72: 15 type=148 (RBDIHS) 5 4 6 9 72: 16 type=149 (RBDIHS) 22 4 6 7 72: 17 type=149 (RBDIHS) 22 4 6 8 72: 18 type=150 (RBDIHS) 0 4 22 24 72: 19 type=151 (RBDIHS) 6 4 22 24 72: 20 type=148 (RBDIHS) 4 6 9 10 72: 21 type=148 (RBDIHS) 4 6 9 11 72: 22 type=152 (RBDIHS) 4 6 9 12 72: 23 type=148 (RBDIHS) 7 6 9 10 72: 24 type=148 (RBDIHS) 7 6 9 11 72: 25 type=148 (RBDIHS) 7 6 9 12 72: 26 type=148 (RBDIHS) 8 6 9 10 72: 27 type=148 (RBDIHS) 8 6 9 11 72: 28 type=148 (RBDIHS) 8 6 9 12 72: 29 type=148 (RBDIHS) 6 9 12 13 72: 30 type=148 (RBDIHS) 6 9 12 14 72: 31 type=152 (RBDIHS) 6 9 12 15 72: 32 type=148 (RBDIHS) 10 9 12 13 72: 33 type=148 (RBDIHS) 10 9 12 14 72: 34 type=148 (RBDIHS) 10 9 12 15 72: 35 type=148 (RBDIHS) 11 9 12 13 72: 36 type=148 (RBDIHS) 11 9 12 14 72: 37 type=148 (RBDIHS) 11 9 12 15 72: 38 type=148 (RBDIHS) 9 12 15 16 72: 39 type=148 (RBDIHS) 9 12 15 17 72: 40 type=153 (RBDIHS) 9 12 15 18 72: 41 type=148 (RBDIHS) 13 12 15 16 72: 42 type=148 (RBDIHS) 13 12 15 17 72: 43 type=154 (RBDIHS) 13 12 15 18 72: 44 type=148 (RBDIHS) 14 12 15 16 72: 45 type=148 (RBDIHS) 14 12 15 17 72: 46 type=154 (RBDIHS) 14 12 15 18 72: 47 type=144 (RBDIHS) 12 15 18 19 72: 48 type=144 (RBDIHS) 12 15 18 20 72: 49 type=144 (RBDIHS) 12 15 18 21 72: 50 type=143 (RBDIHS) 16 15 18 19 72: 51 type=143 (RBDIHS) 16 15 18 20 72: 52 type=143 (RBDIHS) 16 15 18 21 72: 53 type=143 (RBDIHS) 17 15 18 19 72: 54 type=143 (RBDIHS) 17 15 18 20 72: 55 type=143 (RBDIHS) 17 15 18 21 72: 56 type=155 (RBDIHS) 4 22 24 25 72: 57 type=156 (RBDIHS) 4 22 24 26 72: 58 type=155 (RBDIHS) 23 22 24 25 72: 59 type=157 (RBDIHS) 23 22 24 26 72: 60 type=158 (RBDIHS) 22 24 26 28 72: 61 type=159 (RBDIHS) 22 24 26 38 72: 62 type=160 (RBDIHS) 24 26 28 30 72: 63 type=160 (RBDIHS) 24 26 28 34 72: 64 type=161 (RBDIHS) 38 26 28 30 72: 65 type=161 (RBDIHS) 38 26 28 34 72: 66 type=147 (RBDIHS) 24 26 28 29 72: 67 type=148 (RBDIHS) 27 26 28 29 72: 68 type=148 (RBDIHS) 27 26 28 30 72: 69 type=148 (RBDIHS) 27 26 28 34 72: 70 type=149 (RBDIHS) 38 26 28 29 72: 71 type=150 (RBDIHS) 24 26 38 40 72: 72 type=151 (RBDIHS) 28 26 38 40 72: 73 type=148 (RBDIHS) 26 28 30 31 72: 74 type=148 (RBDIHS) 26 28 30 32 72: 75 type=148 (RBDIHS) 26 28 30 33 72: 76 type=148 (RBDIHS) 29 28 30 31 72: 77 type=148 (RBDIHS) 29 28 30 32 72: 78 type=148 (RBDIHS) 29 28 30 33 72: 79 type=148 (RBDIHS) 34 28 30 31 72: 80 type=148 (RBDIHS) 34 28 30 32 72: 81 type=148 (RBDIHS) 34 28 30 33 72: 82 type=148 (RBDIHS) 26 28 34 35 72: 83 type=148 (RBDIHS) 26 28 34 36 72: 84 type=148 (RBDIHS) 26 28 34 37 72: 85 type=148 (RBDIHS) 29 28 34 35 72: 86 type=148 (RBDIHS) 29 28 34 36 72: 87 type=148 (RBDIHS) 29 28 34 37 72: 88 type=148 (RBDIHS) 30 28 34 35 72: 89 type=148 (RBDIHS) 30 28 34 36 72: 90 type=148 (RBDIHS) 30 28 34 37 72: 91 type=155 (RBDIHS) 26 38 40 41 72: 92 type=156 (RBDIHS) 26 38 40 42 72: 93 type=155 (RBDIHS) 39 38 40 41 72: 94 type=157 (RBDIHS) 39 38 40 42 72: 95 type=158 (RBDIHS) 38 40 42 44 72: 96 type=159 (RBDIHS) 38 40 42 58 72: 97 type=147 (RBDIHS) 40 42 44 45 72: 98 type=147 (RBDIHS) 40 42 44 46 72: 99 type=162 (RBDIHS) 40 42 44 47 72: 100 type=148 (RBDIHS) 43 42 44 45 72: 101 type=148 (RBDIHS) 43 42 44 46 72: 102 type=163 (RBDIHS) 43 42 44 47 72: 103 type=149 (RBDIHS) 58 42 44 45 72: 104 type=149 (RBDIHS) 58 42 44 46 72: 105 type=164 (RBDIHS) 58 42 44 47 72: 106 type=150 (RBDIHS) 40 42 58 60 72: 107 type=151 (RBDIHS) 44 42 58 60 72: 108 type=165 (RBDIHS) 44 47 48 49 72: 109 type=165 (RBDIHS) 44 47 48 52 72: 110 type=165 (RBDIHS) 50 47 48 49 72: 111 type=165 (RBDIHS) 50 47 48 52 72: 112 type=165 (RBDIHS) 44 47 50 51 72: 113 type=165 (RBDIHS) 44 47 50 54 72: 114 type=165 (RBDIHS) 48 47 50 51 72: 115 type=165 (RBDIHS) 48 47 50 54 72: 116 type=165 (RBDIHS) 47 48 52 53 72: 117 type=165 (RBDIHS) 47 48 52 56 72: 118 type=165 (RBDIHS) 49 48 52 53 72: 119 type=165 (RBDIHS) 49 48 52 56 72: 120 type=165 (RBDIHS) 47 50 54 55 72: 121 type=165 (RBDIHS) 47 50 54 56 72: 122 type=165 (RBDIHS) 51 50 54 55 72: 123 type=165 (RBDIHS) 51 50 54 56 72: 124 type=165 (RBDIHS) 48 52 56 54 72: 125 type=165 (RBDIHS) 48 52 56 57 72: 126 type=165 (RBDIHS) 53 52 56 54 72: 127 type=165 (RBDIHS) 53 52 56 57 72: 128 type=165 (RBDIHS) 50 54 56 52 72: 129 type=165 (RBDIHS) 50 54 56 57 72: 130 type=165 (RBDIHS) 55 54 56 52 72: 131 type=165 (RBDIHS) 55 54 56 57 72: 132 type=155 (RBDIHS) 42 58 60 61 72: 133 type=156 (RBDIHS) 42 58 60 62 72: 134 type=155 (RBDIHS) 59 58 60 61 72: 135 type=157 (RBDIHS) 59 58 60 62 72: 136 type=159 (RBDIHS) 58 60 62 65 72: 137 type=150 (RBDIHS) 60 62 65 67 72: 138 type=155 (RBDIHS) 62 65 67 68 72: 139 type=156 (RBDIHS) 62 65 67 69 72: 140 type=155 (RBDIHS) 66 65 67 68 72: 141 type=157 (RBDIHS) 66 65 67 69 72: 142 type=158 (RBDIHS) 65 67 69 71 72: 143 type=159 (RBDIHS) 65 67 69 89 72: 144 type=166 (RBDIHS) 67 69 71 74 72: 145 type=167 (RBDIHS) 89 69 71 74 72: 146 type=147 (RBDIHS) 67 69 71 72 72: 147 type=147 (RBDIHS) 67 69 71 73 72: 148 type=148 (RBDIHS) 70 69 71 72 72: 149 type=148 (RBDIHS) 70 69 71 73 72: 150 type=148 (RBDIHS) 70 69 71 74 72: 151 type=149 (RBDIHS) 89 69 71 72 72: 152 type=149 (RBDIHS) 89 69 71 73 72: 153 type=150 (RBDIHS) 67 69 89 91 72: 154 type=151 (RBDIHS) 71 69 89 91 72: 155 type=148 (RBDIHS) 69 71 74 75 72: 156 type=148 (RBDIHS) 69 71 74 76 72: 157 type=152 (RBDIHS) 69 71 74 77 72: 158 type=148 (RBDIHS) 72 71 74 75 72: 159 type=148 (RBDIHS) 72 71 74 76 72: 160 type=148 (RBDIHS) 72 71 74 77 72: 161 type=148 (RBDIHS) 73 71 74 75 72: 162 type=148 (RBDIHS) 73 71 74 76 72: 163 type=148 (RBDIHS) 73 71 74 77 72: 164 type=148 (RBDIHS) 71 74 77 78 72: 165 type=148 (RBDIHS) 71 74 77 79 72: 166 type=153 (RBDIHS) 71 74 77 80 72: 167 type=148 (RBDIHS) 75 74 77 78 72: 168 type=148 (RBDIHS) 75 74 77 79 72: 169 type=168 (RBDIHS) 75 74 77 80 72: 170 type=148 (RBDIHS) 76 74 77 78 72: 171 type=148 (RBDIHS) 76 74 77 79 72: 172 type=168 (RBDIHS) 76 74 77 80 72: 173 type=169 (RBDIHS) 74 77 80 81 72: 174 type=170 (RBDIHS) 74 77 80 82 72: 175 type=171 (RBDIHS) 78 77 80 82 72: 176 type=171 (RBDIHS) 79 77 80 82 72: 177 type=172 (RBDIHS) 77 80 82 83 72: 178 type=172 (RBDIHS) 77 80 82 86 72: 179 type=173 (RBDIHS) 81 80 82 83 72: 180 type=173 (RBDIHS) 81 80 82 86 72: 181 type=173 (RBDIHS) 80 82 83 84 72: 182 type=173 (RBDIHS) 80 82 83 85 72: 183 type=173 (RBDIHS) 86 82 83 84 72: 184 type=173 (RBDIHS) 86 82 83 85 72: 185 type=173 (RBDIHS) 80 82 86 87 72: 186 type=173 (RBDIHS) 80 82 86 88 72: 187 type=173 (RBDIHS) 83 82 86 87 72: 188 type=173 (RBDIHS) 83 82 86 88 72: 189 type=155 (RBDIHS) 69 89 91 92 72: 190 type=156 (RBDIHS) 69 89 91 93 72: 191 type=155 (RBDIHS) 90 89 91 92 72: 192 type=157 (RBDIHS) 90 89 91 93 72: 193 type=158 (RBDIHS) 89 91 93 95 72: 194 type=159 (RBDIHS) 89 91 93 100 72: 195 type=174 (RBDIHS) 91 93 95 98 72: 196 type=175 (RBDIHS) 100 93 95 98 72: 197 type=147 (RBDIHS) 91 93 95 96 72: 198 type=147 (RBDIHS) 91 93 95 97 72: 199 type=148 (RBDIHS) 94 93 95 96 72: 200 type=148 (RBDIHS) 94 93 95 97 72: 201 type=176 (RBDIHS) 94 93 95 98 72: 202 type=149 (RBDIHS) 100 93 95 96 72: 203 type=149 (RBDIHS) 100 93 95 97 72: 204 type=150 (RBDIHS) 91 93 100 102 72: 205 type=151 (RBDIHS) 95 93 100 102 72: 206 type=177 (RBDIHS) 93 95 98 99 72: 207 type=178 (RBDIHS) 96 95 98 99 72: 208 type=178 (RBDIHS) 97 95 98 99 72: 209 type=155 (RBDIHS) 93 100 102 103 72: 210 type=156 (RBDIHS) 93 100 102 104 72: 211 type=155 (RBDIHS) 101 100 102 103 72: 212 type=157 (RBDIHS) 101 100 102 104 72: 213 type=158 (RBDIHS) 100 102 104 106 72: 214 type=159 (RBDIHS) 100 102 104 115 72: 215 type=179 (RBDIHS) 102 104 106 109 72: 216 type=180 (RBDIHS) 115 104 106 109 72: 217 type=147 (RBDIHS) 102 104 106 107 72: 218 type=147 (RBDIHS) 102 104 106 108 72: 219 type=148 (RBDIHS) 105 104 106 107 72: 220 type=148 (RBDIHS) 105 104 106 108 72: 221 type=148 (RBDIHS) 105 104 106 109 72: 222 type=149 (RBDIHS) 115 104 106 107 72: 223 type=149 (RBDIHS) 115 104 106 108 72: 224 type=150 (RBDIHS) 102 104 115 117 72: 225 type=151 (RBDIHS) 106 104 115 117 72: 226 type=148 (RBDIHS) 104 106 109 110 72: 227 type=148 (RBDIHS) 104 106 109 111 72: 228 type=181 (RBDIHS) 104 106 109 112 72: 229 type=148 (RBDIHS) 107 106 109 110 72: 230 type=148 (RBDIHS) 107 106 109 111 72: 231 type=182 (RBDIHS) 107 106 109 112 72: 232 type=148 (RBDIHS) 108 106 109 110 72: 233 type=148 (RBDIHS) 108 106 109 111 72: 234 type=182 (RBDIHS) 108 106 109 112 72: 235 type=183 (RBDIHS) 106 109 112 113 72: 236 type=183 (RBDIHS) 106 109 112 114 72: 237 type=155 (RBDIHS) 104 115 117 118 72: 238 type=156 (RBDIHS) 104 115 117 119 72: 239 type=155 (RBDIHS) 116 115 117 118 72: 240 type=157 (RBDIHS) 116 115 117 119 72: 241 type=158 (RBDIHS) 115 117 119 121 72: 242 type=159 (RBDIHS) 115 117 119 134 72: 243 type=184 (RBDIHS) 117 119 121 124 72: 244 type=185 (RBDIHS) 134 119 121 124 72: 245 type=147 (RBDIHS) 117 119 121 122 72: 246 type=147 (RBDIHS) 117 119 121 123 72: 247 type=148 (RBDIHS) 120 119 121 122 72: 248 type=148 (RBDIHS) 120 119 121 123 72: 249 type=148 (RBDIHS) 120 119 121 124 72: 250 type=149 (RBDIHS) 134 119 121 122 72: 251 type=149 (RBDIHS) 134 119 121 123 72: 252 type=150 (RBDIHS) 117 119 134 136 72: 253 type=151 (RBDIHS) 121 119 134 136 72: 254 type=148 (RBDIHS) 119 121 124 125 72: 255 type=152 (RBDIHS) 119 121 124 126 72: 256 type=152 (RBDIHS) 119 121 124 130 72: 257 type=148 (RBDIHS) 122 121 124 125 72: 258 type=148 (RBDIHS) 122 121 124 126 72: 259 type=148 (RBDIHS) 122 121 124 130 72: 260 type=148 (RBDIHS) 123 121 124 125 72: 261 type=148 (RBDIHS) 123 121 124 126 72: 262 type=148 (RBDIHS) 123 121 124 130 72: 263 type=148 (RBDIHS) 121 124 126 127 72: 264 type=148 (RBDIHS) 121 124 126 128 72: 265 type=148 (RBDIHS) 121 124 126 129 72: 266 type=148 (RBDIHS) 125 124 126 127 72: 267 type=148 (RBDIHS) 125 124 126 128 72: 268 type=148 (RBDIHS) 125 124 126 129 72: 269 type=148 (RBDIHS) 130 124 126 127 72: 270 type=148 (RBDIHS) 130 124 126 128 72: 271 type=148 (RBDIHS) 130 124 126 129 72: 272 type=148 (RBDIHS) 121 124 130 131 72: 273 type=148 (RBDIHS) 121 124 130 132 72: 274 type=148 (RBDIHS) 121 124 130 133 72: 275 type=148 (RBDIHS) 125 124 130 131 72: 276 type=148 (RBDIHS) 125 124 130 132 72: 277 type=148 (RBDIHS) 125 124 130 133 72: 278 type=148 (RBDIHS) 126 124 130 131 72: 279 type=148 (RBDIHS) 126 124 130 132 72: 280 type=148 (RBDIHS) 126 124 130 133 72: 281 type=155 (RBDIHS) 119 134 136 137 72: 282 type=156 (RBDIHS) 119 134 136 138 72: 283 type=155 (RBDIHS) 135 134 136 137 72: 284 type=157 (RBDIHS) 135 134 136 138 72: 285 type=158 (RBDIHS) 134 136 138 140 72: 286 type=159 (RBDIHS) 134 136 138 144 72: 287 type=147 (RBDIHS) 136 138 140 141 72: 288 type=147 (RBDIHS) 136 138 140 142 72: 289 type=147 (RBDIHS) 136 138 140 143 72: 290 type=148 (RBDIHS) 139 138 140 141 72: 291 type=148 (RBDIHS) 139 138 140 142 72: 292 type=148 (RBDIHS) 139 138 140 143 72: 293 type=149 (RBDIHS) 144 138 140 141 72: 294 type=149 (RBDIHS) 144 138 140 142 72: 295 type=149 (RBDIHS) 144 138 140 143 72: 296 type=150 (RBDIHS) 136 138 144 146 72: 297 type=151 (RBDIHS) 140 138 144 146 72: 298 type=155 (RBDIHS) 138 144 146 147 72: 299 type=156 (RBDIHS) 138 144 146 148 72: 300 type=155 (RBDIHS) 145 144 146 147 72: 301 type=157 (RBDIHS) 145 144 146 148 72: 302 type=158 (RBDIHS) 144 146 148 150 72: 303 type=159 (RBDIHS) 144 146 148 154 72: 304 type=147 (RBDIHS) 146 148 150 151 72: 305 type=147 (RBDIHS) 146 148 150 152 72: 306 type=147 (RBDIHS) 146 148 150 153 72: 307 type=148 (RBDIHS) 149 148 150 151 72: 308 type=148 (RBDIHS) 149 148 150 152 72: 309 type=148 (RBDIHS) 149 148 150 153 72: 310 type=149 (RBDIHS) 154 148 150 151 72: 311 type=149 (RBDIHS) 154 148 150 152 72: 312 type=149 (RBDIHS) 154 148 150 153 72: Restr. Dih.: 72: nr: 0 72: CBT Dih.: 72: nr: 0 72: Fourier Dih.: 72: nr: 0 72: Improper Dih.: 72: nr: 0 72: Per. Imp. Dih.: 72: nr: 0 72: Tab. Dih.: 72: nr: 0 72: CMAP Dih.: 72: nr: 0 72: GB 1-2 Pol.: 72: nr: 0 72: GB 1-3 Pol.: 72: nr: 0 72: GB 1-4 Pol.: 72: nr: 0 72: GB Polariz.: 72: nr: 0 72: Nonpolar Sol.: 72: nr: 0 72: LJ-14: 72: nr: 1197 72: iatoms: 72: 0 type=186 (LJ14) 0 7 72: 1 type=186 (LJ14) 0 8 72: 2 type=187 (LJ14) 0 9 72: 3 type=188 (LJ14) 0 23 72: 4 type=189 (LJ14) 0 24 72: 5 type=190 (LJ14) 1 5 72: 6 type=190 (LJ14) 1 6 72: 7 type=190 (LJ14) 1 22 72: 8 type=190 (LJ14) 2 5 72: 9 type=190 (LJ14) 2 6 72: 10 type=190 (LJ14) 2 22 72: 11 type=190 (LJ14) 3 5 72: 12 type=190 (LJ14) 3 6 72: 13 type=190 (LJ14) 3 22 72: 14 type=191 (LJ14) 4 10 72: 15 type=191 (LJ14) 4 11 72: 16 type=192 (LJ14) 4 12 72: 17 type=190 (LJ14) 4 25 72: 18 type=192 (LJ14) 4 26 72: 19 type=193 (LJ14) 5 7 72: 20 type=193 (LJ14) 5 8 72: 21 type=191 (LJ14) 5 9 72: 22 type=194 (LJ14) 5 23 72: 23 type=186 (LJ14) 5 24 72: 24 type=191 (LJ14) 6 13 72: 25 type=191 (LJ14) 6 14 72: 26 type=192 (LJ14) 6 15 72: 27 type=195 (LJ14) 6 23 72: 28 type=187 (LJ14) 6 24 72: 29 type=193 (LJ14) 7 10 72: 30 type=193 (LJ14) 7 11 72: 31 type=191 (LJ14) 7 12 72: 32 type=196 (LJ14) 7 22 72: 33 type=193 (LJ14) 8 10 72: 34 type=193 (LJ14) 8 11 72: 35 type=191 (LJ14) 8 12 72: 36 type=196 (LJ14) 8 22 72: 37 type=191 (LJ14) 9 16 72: 38 type=191 (LJ14) 9 17 72: 39 type=187 (LJ14) 9 18 72: 40 type=197 (LJ14) 9 22 72: 41 type=193 (LJ14) 10 13 72: 42 type=193 (LJ14) 10 14 72: 43 type=191 (LJ14) 10 15 72: 44 type=193 (LJ14) 11 13 72: 45 type=193 (LJ14) 11 14 72: 46 type=191 (LJ14) 11 15 72: 47 type=190 (LJ14) 12 19 72: 48 type=190 (LJ14) 12 20 72: 49 type=190 (LJ14) 12 21 72: 50 type=193 (LJ14) 13 16 72: 51 type=193 (LJ14) 13 17 72: 52 type=186 (LJ14) 13 18 72: 53 type=193 (LJ14) 14 16 72: 54 type=193 (LJ14) 14 17 72: 55 type=186 (LJ14) 14 18 72: 56 type=190 (LJ14) 16 19 72: 57 type=190 (LJ14) 16 20 72: 58 type=190 (LJ14) 16 21 72: 59 type=190 (LJ14) 17 19 72: 60 type=190 (LJ14) 17 20 72: 61 type=190 (LJ14) 17 21 72: 62 type=196 (LJ14) 22 27 72: 63 type=197 (LJ14) 22 28 72: 64 type=198 (LJ14) 22 38 72: 65 type=190 (LJ14) 23 25 72: 66 type=195 (LJ14) 23 26 72: 67 type=186 (LJ14) 24 29 72: 68 type=187 (LJ14) 24 30 72: 69 type=187 (LJ14) 24 34 72: 70 type=188 (LJ14) 24 39 72: 71 type=189 (LJ14) 24 40 72: 72 type=190 (LJ14) 25 27 72: 73 type=190 (LJ14) 25 28 72: 74 type=190 (LJ14) 25 38 72: 75 type=191 (LJ14) 26 31 72: 76 type=191 (LJ14) 26 32 72: 77 type=191 (LJ14) 26 33 72: 78 type=191 (LJ14) 26 35 72: 79 type=191 (LJ14) 26 36 72: 80 type=191 (LJ14) 26 37 72: 81 type=190 (LJ14) 26 41 72: 82 type=192 (LJ14) 26 42 72: 83 type=193 (LJ14) 27 29 72: 84 type=191 (LJ14) 27 30 72: 85 type=191 (LJ14) 27 34 72: 86 type=194 (LJ14) 27 39 72: 87 type=186 (LJ14) 27 40 72: 88 type=195 (LJ14) 28 39 72: 89 type=187 (LJ14) 28 40 72: 90 type=193 (LJ14) 29 31 72: 91 type=193 (LJ14) 29 32 72: 92 type=193 (LJ14) 29 33 72: 93 type=193 (LJ14) 29 35 72: 94 type=193 (LJ14) 29 36 72: 95 type=193 (LJ14) 29 37 72: 96 type=196 (LJ14) 29 38 72: 97 type=191 (LJ14) 30 35 72: 98 type=191 (LJ14) 30 36 72: 99 type=191 (LJ14) 30 37 72: 100 type=197 (LJ14) 30 38 72: 101 type=191 (LJ14) 31 34 72: 102 type=191 (LJ14) 32 34 72: 103 type=191 (LJ14) 33 34 72: 104 type=197 (LJ14) 34 38 72: 105 type=196 (LJ14) 38 43 72: 106 type=197 (LJ14) 38 44 72: 107 type=198 (LJ14) 38 58 72: 108 type=190 (LJ14) 39 41 72: 109 type=195 (LJ14) 39 42 72: 110 type=186 (LJ14) 40 45 72: 111 type=186 (LJ14) 40 46 72: 112 type=199 (LJ14) 40 47 72: 113 type=188 (LJ14) 40 59 72: 114 type=189 (LJ14) 40 60 72: 115 type=190 (LJ14) 41 43 72: 116 type=190 (LJ14) 41 44 72: 117 type=190 (LJ14) 41 58 72: 118 type=200 (LJ14) 42 48 72: 119 type=200 (LJ14) 42 50 72: 120 type=190 (LJ14) 42 61 72: 121 type=192 (LJ14) 42 62 72: 122 type=193 (LJ14) 43 45 72: 123 type=193 (LJ14) 43 46 72: 124 type=201 (LJ14) 43 47 72: 125 type=194 (LJ14) 43 59 72: 126 type=186 (LJ14) 43 60 72: 127 type=202 (LJ14) 44 49 72: 128 type=202 (LJ14) 44 51 72: 129 type=200 (LJ14) 44 52 72: 130 type=200 (LJ14) 44 54 72: 131 type=195 (LJ14) 44 59 72: 132 type=187 (LJ14) 44 60 72: 133 type=201 (LJ14) 45 48 72: 134 type=201 (LJ14) 45 50 72: 135 type=196 (LJ14) 45 58 72: 136 type=201 (LJ14) 46 48 72: 137 type=201 (LJ14) 46 50 72: 138 type=196 (LJ14) 46 58 72: 139 type=203 (LJ14) 47 53 72: 140 type=203 (LJ14) 47 55 72: 141 type=204 (LJ14) 47 56 72: 142 type=205 (LJ14) 47 58 72: 143 type=203 (LJ14) 48 51 72: 144 type=204 (LJ14) 48 54 72: 145 type=203 (LJ14) 48 57 72: 146 type=203 (LJ14) 49 50 72: 147 type=206 (LJ14) 49 53 72: 148 type=203 (LJ14) 49 56 72: 149 type=204 (LJ14) 50 52 72: 150 type=203 (LJ14) 50 57 72: 151 type=206 (LJ14) 51 55 72: 152 type=203 (LJ14) 51 56 72: 153 type=203 (LJ14) 52 55 72: 154 type=203 (LJ14) 53 54 72: 155 type=206 (LJ14) 53 57 72: 156 type=206 (LJ14) 55 57 72: 157 type=196 (LJ14) 58 63 72: 158 type=196 (LJ14) 58 64 72: 159 type=198 (LJ14) 58 65 72: 160 type=190 (LJ14) 59 61 72: 161 type=195 (LJ14) 59 62 72: 162 type=188 (LJ14) 60 66 72: 163 type=189 (LJ14) 60 67 72: 164 type=190 (LJ14) 61 63 72: 165 type=190 (LJ14) 61 64 72: 166 type=190 (LJ14) 61 65 72: 167 type=190 (LJ14) 62 68 72: 168 type=192 (LJ14) 62 69 72: 169 type=194 (LJ14) 63 66 72: 170 type=186 (LJ14) 63 67 72: 171 type=194 (LJ14) 64 66 72: 172 type=186 (LJ14) 64 67 72: 173 type=196 (LJ14) 65 70 72: 174 type=197 (LJ14) 65 71 72: 175 type=198 (LJ14) 65 89 72: 176 type=190 (LJ14) 66 68 72: 177 type=195 (LJ14) 66 69 72: 178 type=186 (LJ14) 67 72 72: 179 type=186 (LJ14) 67 73 72: 180 type=187 (LJ14) 67 74 72: 181 type=188 (LJ14) 67 90 72: 182 type=189 (LJ14) 67 91 72: 183 type=190 (LJ14) 68 70 72: 184 type=190 (LJ14) 68 71 72: 185 type=190 (LJ14) 68 89 72: 186 type=191 (LJ14) 69 75 72: 187 type=191 (LJ14) 69 76 72: 188 type=192 (LJ14) 69 77 72: 189 type=190 (LJ14) 69 92 72: 190 type=192 (LJ14) 69 93 72: 191 type=193 (LJ14) 70 72 72: 192 type=193 (LJ14) 70 73 72: 193 type=191 (LJ14) 70 74 72: 194 type=194 (LJ14) 70 90 72: 195 type=186 (LJ14) 70 91 72: 196 type=191 (LJ14) 71 78 72: 197 type=191 (LJ14) 71 79 72: 198 type=187 (LJ14) 71 80 72: 199 type=195 (LJ14) 71 90 72: 200 type=187 (LJ14) 71 91 72: 201 type=193 (LJ14) 72 75 72: 202 type=193 (LJ14) 72 76 72: 203 type=191 (LJ14) 72 77 72: 204 type=196 (LJ14) 72 89 72: 205 type=193 (LJ14) 73 75 72: 206 type=193 (LJ14) 73 76 72: 207 type=191 (LJ14) 73 77 72: 208 type=196 (LJ14) 73 89 72: 209 type=190 (LJ14) 74 81 72: 210 type=207 (LJ14) 74 82 72: 211 type=197 (LJ14) 74 89 72: 212 type=193 (LJ14) 75 78 72: 213 type=193 (LJ14) 75 79 72: 214 type=186 (LJ14) 75 80 72: 215 type=193 (LJ14) 76 78 72: 216 type=193 (LJ14) 76 79 72: 217 type=186 (LJ14) 76 80 72: 218 type=187 (LJ14) 77 83 72: 219 type=187 (LJ14) 77 86 72: 220 type=190 (LJ14) 78 81 72: 221 type=208 (LJ14) 78 82 72: 222 type=190 (LJ14) 79 81 72: 223 type=208 (LJ14) 79 82 72: 224 type=190 (LJ14) 80 84 72: 225 type=190 (LJ14) 80 85 72: 226 type=190 (LJ14) 80 87 72: 227 type=190 (LJ14) 80 88 72: 228 type=190 (LJ14) 81 83 72: 229 type=190 (LJ14) 81 86 72: 230 type=190 (LJ14) 83 87 72: 231 type=190 (LJ14) 83 88 72: 232 type=190 (LJ14) 84 86 72: 233 type=190 (LJ14) 85 86 72: 234 type=196 (LJ14) 89 94 72: 235 type=197 (LJ14) 89 95 72: 236 type=198 (LJ14) 89 100 72: 237 type=190 (LJ14) 90 92 72: 238 type=195 (LJ14) 90 93 72: 239 type=186 (LJ14) 91 96 72: 240 type=186 (LJ14) 91 97 72: 241 type=209 (LJ14) 91 98 72: 242 type=188 (LJ14) 91 101 72: 243 type=189 (LJ14) 91 102 72: 244 type=190 (LJ14) 92 94 72: 245 type=190 (LJ14) 92 95 72: 246 type=190 (LJ14) 92 100 72: 247 type=190 (LJ14) 93 99 72: 248 type=190 (LJ14) 93 103 72: 249 type=192 (LJ14) 93 104 72: 250 type=193 (LJ14) 94 96 72: 251 type=193 (LJ14) 94 97 72: 252 type=210 (LJ14) 94 98 72: 253 type=194 (LJ14) 94 101 72: 254 type=186 (LJ14) 94 102 72: 255 type=195 (LJ14) 95 101 72: 256 type=187 (LJ14) 95 102 72: 257 type=190 (LJ14) 96 99 72: 258 type=196 (LJ14) 96 100 72: 259 type=190 (LJ14) 97 99 72: 260 type=196 (LJ14) 97 100 72: 261 type=211 (LJ14) 98 100 72: 262 type=196 (LJ14) 100 105 72: 263 type=197 (LJ14) 100 106 72: 264 type=198 (LJ14) 100 115 72: 265 type=190 (LJ14) 101 103 72: 266 type=195 (LJ14) 101 104 72: 267 type=186 (LJ14) 102 107 72: 268 type=186 (LJ14) 102 108 72: 269 type=187 (LJ14) 102 109 72: 270 type=188 (LJ14) 102 116 72: 271 type=189 (LJ14) 102 117 72: 272 type=190 (LJ14) 103 105 72: 273 type=190 (LJ14) 103 106 72: 274 type=190 (LJ14) 103 115 72: 275 type=191 (LJ14) 104 110 72: 276 type=191 (LJ14) 104 111 72: 277 type=197 (LJ14) 104 112 72: 278 type=190 (LJ14) 104 118 72: 279 type=192 (LJ14) 104 119 72: 280 type=193 (LJ14) 105 107 72: 281 type=193 (LJ14) 105 108 72: 282 type=191 (LJ14) 105 109 72: 283 type=194 (LJ14) 105 116 72: 284 type=186 (LJ14) 105 117 72: 285 type=195 (LJ14) 106 113 72: 286 type=195 (LJ14) 106 114 72: 287 type=195 (LJ14) 106 116 72: 288 type=187 (LJ14) 106 117 72: 289 type=193 (LJ14) 107 110 72: 290 type=193 (LJ14) 107 111 72: 291 type=196 (LJ14) 107 112 72: 292 type=196 (LJ14) 107 115 72: 293 type=193 (LJ14) 108 110 72: 294 type=193 (LJ14) 108 111 72: 295 type=196 (LJ14) 108 112 72: 296 type=196 (LJ14) 108 115 72: 297 type=197 (LJ14) 109 115 72: 298 type=194 (LJ14) 110 113 72: 299 type=194 (LJ14) 110 114 72: 300 type=194 (LJ14) 111 113 72: 301 type=194 (LJ14) 111 114 72: 302 type=196 (LJ14) 115 120 72: 303 type=197 (LJ14) 115 121 72: 304 type=198 (LJ14) 115 134 72: 305 type=190 (LJ14) 116 118 72: 306 type=195 (LJ14) 116 119 72: 307 type=186 (LJ14) 117 122 72: 308 type=186 (LJ14) 117 123 72: 309 type=187 (LJ14) 117 124 72: 310 type=188 (LJ14) 117 135 72: 311 type=189 (LJ14) 117 136 72: 312 type=190 (LJ14) 118 120 72: 313 type=190 (LJ14) 118 121 72: 314 type=190 (LJ14) 118 134 72: 315 type=191 (LJ14) 119 125 72: 316 type=192 (LJ14) 119 126 72: 317 type=192 (LJ14) 119 130 72: 318 type=190 (LJ14) 119 137 72: 319 type=192 (LJ14) 119 138 72: 320 type=193 (LJ14) 120 122 72: 321 type=193 (LJ14) 120 123 72: 322 type=191 (LJ14) 120 124 72: 323 type=194 (LJ14) 120 135 72: 324 type=186 (LJ14) 120 136 72: 325 type=191 (LJ14) 121 127 72: 326 type=191 (LJ14) 121 128 72: 327 type=191 (LJ14) 121 129 72: 328 type=191 (LJ14) 121 131 72: 329 type=191 (LJ14) 121 132 72: 330 type=191 (LJ14) 121 133 72: 331 type=195 (LJ14) 121 135 72: 332 type=187 (LJ14) 121 136 72: 333 type=193 (LJ14) 122 125 72: 334 type=191 (LJ14) 122 126 72: 335 type=191 (LJ14) 122 130 72: 336 type=196 (LJ14) 122 134 72: 337 type=193 (LJ14) 123 125 72: 338 type=191 (LJ14) 123 126 72: 339 type=191 (LJ14) 123 130 72: 340 type=196 (LJ14) 123 134 72: 341 type=197 (LJ14) 124 134 72: 342 type=193 (LJ14) 125 127 72: 343 type=193 (LJ14) 125 128 72: 344 type=193 (LJ14) 125 129 72: 345 type=193 (LJ14) 125 131 72: 346 type=193 (LJ14) 125 132 72: 347 type=193 (LJ14) 125 133 72: 348 type=191 (LJ14) 126 131 72: 349 type=191 (LJ14) 126 132 72: 350 type=191 (LJ14) 126 133 72: 351 type=191 (LJ14) 127 130 72: 352 type=191 (LJ14) 128 130 72: 353 type=191 (LJ14) 129 130 72: 354 type=196 (LJ14) 134 139 72: 355 type=197 (LJ14) 134 140 72: 356 type=198 (LJ14) 134 144 72: 357 type=190 (LJ14) 135 137 72: 358 type=195 (LJ14) 135 138 72: 359 type=186 (LJ14) 136 141 72: 360 type=186 (LJ14) 136 142 72: 361 type=186 (LJ14) 136 143 72: 362 type=188 (LJ14) 136 145 72: 363 type=189 (LJ14) 136 146 72: 364 type=190 (LJ14) 137 139 72: 365 type=190 (LJ14) 137 140 72: 366 type=190 (LJ14) 137 144 72: 367 type=190 (LJ14) 138 147 72: 368 type=192 (LJ14) 138 148 72: 369 type=193 (LJ14) 139 141 72: 370 type=193 (LJ14) 139 142 72: 371 type=193 (LJ14) 139 143 72: 372 type=194 (LJ14) 139 145 72: 373 type=186 (LJ14) 139 146 72: 374 type=195 (LJ14) 140 145 72: 375 type=187 (LJ14) 140 146 72: 376 type=196 (LJ14) 141 144 72: 377 type=196 (LJ14) 142 144 72: 378 type=196 (LJ14) 143 144 72: 379 type=196 (LJ14) 144 149 72: 380 type=197 (LJ14) 144 150 72: 381 type=198 (LJ14) 144 154 72: 382 type=190 (LJ14) 145 147 72: 383 type=195 (LJ14) 145 148 72: 384 type=186 (LJ14) 146 151 72: 385 type=186 (LJ14) 146 152 72: 386 type=186 (LJ14) 146 153 72: 387 type=188 (LJ14) 146 155 72: 388 type=190 (LJ14) 147 149 72: 389 type=190 (LJ14) 147 150 72: 390 type=190 (LJ14) 147 154 72: 391 type=193 (LJ14) 149 151 72: 392 type=193 (LJ14) 149 152 72: 393 type=193 (LJ14) 149 153 72: 394 type=194 (LJ14) 149 155 72: 395 type=195 (LJ14) 150 155 72: 396 type=196 (LJ14) 151 154 72: 397 type=196 (LJ14) 152 154 72: 398 type=196 (LJ14) 153 154 72: Coulomb-14: 72: nr: 0 72: LJC-14 q: 72: nr: 0 72: LJC Pairs NB: 72: nr: 0 72: LJ (SR): 72: nr: 0 72: Buck.ham (SR): 72: nr: 0 72: LJ: 72: nr: 0 72: B.ham: 72: nr: 0 72: Disper. corr.: 72: nr: 0 72: Coulomb (SR): 72: nr: 0 72: Coul: 72: nr: 0 72: RF excl.: 72: nr: 0 72: Coul. recip.: 72: nr: 0 72: LJ recip.: 72: nr: 0 72: DPD: 72: nr: 0 72: Polarization: 72: nr: 0 72: Water Pol.: 72: nr: 0 72: Thole Pol.: 72: nr: 0 72: Anharm. Pol.: 72: nr: 0 72: Position Rest.: 72: nr: 0 72: Flat-b. P-R.: 72: nr: 0 72: Dis. Rest.: 72: nr: 0 72: D.R.Viol. (nm): 72: nr: 0 72: Orient. Rest.: 72: nr: 0 72: Ori. R. RMSD: 72: nr: 0 72: Angle Rest.: 72: nr: 0 72: Angle Rest. Z: 72: nr: 0 72: Dih. Rest.: 72: nr: 0 72: Dih. Rest. Vi.: 72: nr: 0 72: Constraint: 72: nr: 0 72: Constr. No Co.: 72: nr: 0 72: Settle: 72: nr: 0 72: Virtual site 1: 72: nr: 0 72: Virtual site 2: 72: nr: 0 72: Virt. site 2fd: 72: nr: 0 72: Virtual site 3: 72: nr: 0 72: Virt. site 3fd: 72: nr: 0 72: Vir. site 3fad: 72: nr: 0 72: Vir. site 3out: 72: nr: 0 72: Virt. site 4fd: 72: nr: 0 72: Vir. site 4fdn: 72: nr: 0 72: Virtual site N: 72: nr: 0 72: COM Pull En.: 72: nr: 0 72: Dens. fitting: 72: nr: 0 72: Quantum En.: 72: nr: 0 72: NN Potential: 72: nr: 0 72: Potential: 72: nr: 0 72: Kinetic En.: 72: nr: 0 72: Total Energy: 72: nr: 0 72: Conserved En.: 72: nr: 0 72: Temperature: 72: nr: 0 72: Vir. Temp.: 72: nr: 0 72: Pres. DC: 72: nr: 0 72: Pressure: 72: nr: 0 72: dH/dl constr.: 72: nr: 0 72: dVremain/dl: 72: nr: 0 72: dEkin/dl: 72: nr: 0 72: dVcoul/dl: 72: nr: 0 72: dVvdw/dl: 72: nr: 0 72: dVbonded/dl: 72: nr: 0 72: dVrestraint/dl: 72: nr: 0 72: dVtemp/dl: 72: nr: 0 72: grp[T-Coupling ] nr=1, name=[ rest] 72: grp[Energy Mon. ] nr=1, name=[ rest] 72: grp[Acc. not used] nr=1, name=[ rest] 72: grp[Freeze ] nr=1, name=[ rest] 72: grp[User1 ] nr=1, name=[ rest] 72: grp[User2 ] nr=1, name=[ rest] 72: grp[VCM ] nr=1, name=[ rest] 72: grp[Compressed X] nr=1, name=[ rest] 72: grp[Or. Res. Fit] nr=1, name=[ rest] 72: grp[QMMM ] nr=1, name=[ rest] 72: grpname (11): 72: grpname[0]={name="System"} 72: grpname[1]={name="Protein"} 72: grpname[2]={name="Protein-H"} 72: grpname[3]={name="C-alpha"} 72: grpname[4]={name="Backbone"} 72: grpname[5]={name="MainChain"} 72: grpname[6]={name="MainChain+Cb"} 72: grpname[7]={name="MainChain+H"} 72: grpname[8]={name="SideChain"} 72: grpname[9]={name="SideChain-H"} 72: grpname[10]={name="rest"} 72: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 72: allocated 0 0 0 0 0 0 0 0 0 0 72: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 72: box (3x3): 72: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 72: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 72: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 72: box_rel (3x3): 72: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv (3x3): 72: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev (3x3): 72: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev (3x3): 72: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev (3x3): 72: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: nosehoover_xi: not available 72: x (156x3): 72: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 72: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 72: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 72: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 72: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 72: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 72: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 72: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 72: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 72: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 72: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 72: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 72: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 72: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 72: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 72: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 72: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 72: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 72: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 72: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 72: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 72: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 72: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 72: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 72: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 72: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 72: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 72: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 72: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 72: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 72: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 72: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 72: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 72: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 72: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 72: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 72: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 72: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 72: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 72: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 72: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 72: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 72: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 72: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 72: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 72: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 72: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 72: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 72: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 72: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 72: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 72: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 72: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 72: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 72: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 72: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 72: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 72: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 72: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 72: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 72: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 72: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 72: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 72: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 72: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 72: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 72: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 72: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 72: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 72: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 72: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 72: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 72: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 72: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 72: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 72: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 72: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 72: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 72: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 72: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 72: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 72: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 72: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 72: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 72: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 72: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 72: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 72: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 72: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 72: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 72: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 72: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 72: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 72: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 72: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 72: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 72: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 72: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 72: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 72: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 72: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 72: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 72: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 72: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 72: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 72: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 72: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 72: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 72: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 72: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 72: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 72: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 72: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 72: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 72: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 72: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 72: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 72: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 72: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 72: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 72: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 72: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 72: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 72: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 72: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 72: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 72: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 72: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 72: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 72: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 72: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 72: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 72: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 72: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 72: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 72: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 72: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 72: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 72: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 72: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 72: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 72: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 72: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 72: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 72: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 72: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 72: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 72: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 72: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 72: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 72: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 72: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 72: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 72: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 72: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 72: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 72: v (156x3): 72: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: Group statistics 72: T-Coupling : 156 (total 156 atoms) 72: Energy Mon. : 156 (total 156 atoms) 72: Acc. not used: 156 (total 156 atoms) 72: Freeze : 156 (total 156 atoms) 72: User1 : 156 (total 156 atoms) 72: User2 : 156 (total 156 atoms) 72: VCM : 156 (total 156 atoms) 72: Compressed X: 156 (total 156 atoms) 72: Or. Res. Fit: 156 (total 156 atoms) 72: QMMM : 156 (total 156 atoms) 72: [ OK ] DumpTest.WorksWithTpr (6 ms) 72: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 72: [----------] 2 tests from DumpTest (7 ms total) 72: 72: [----------] 3 tests from HelpwritingTest 72: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 72: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 72: [ RUN ] HelpwritingTest.DumpWritesHelp 72: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 72: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 72: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 72: [----------] 3 tests from HelpwritingTest (0 ms total) 72: 72: [----------] 7 tests from GmxMakeNdx 72: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 16 Protein residues 72: Analysing Protein... 72: 72: 0 System : 256 atoms 72: 1 Protein : 256 atoms 72: 2 Protein-H : 139 atoms 72: 3 C-alpha : 16 atoms 72: 4 Backbone : 48 atoms 72: 5 MainChain : 63 atoms 72: 6 MainChain+Cb : 78 atoms 72: 7 MainChain+H : 81 atoms 72: 8 SideChain : 175 atoms 72: 9 SideChain-H : 76 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (1 ms) 72: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 1 'Protein' 72: Copied index group 2 'Protein-H' 72: Merged two groups with OR: 22 10 -> 22 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 72: [ RUN ] GmxMakeNdx.HandlesNotProtein 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 4 'Backbone' 72: Copied index group 8 'SideChain' 72: Merged two groups with AND: 5 13 -> 0 72: Group is empty 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Removed group 0 'System' 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 72: [ RUN ] GmxMakeNdx.Splitres 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into residues 72: 72: > 72: [ OK ] GmxMakeNdx.Splitres (0 ms) 72: [ RUN ] GmxMakeNdx.Splitat 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into atoms 72: 72: > 72: [ OK ] GmxMakeNdx.Splitat (0 ms) 72: [----------] 7 tests from GmxMakeNdx (5 ms total) 72: 72: [----------] 4 tests from ReportMethodsTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -268829081 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectInformation 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 72: [ RUN ] ReportMethodsTest.ToolEndToEndTest 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: section: Methods 72: subsection: Simulation system 72: A system of 1 molecules (156 atoms) was simulated. 72: 72: subsection: Simulation settings 72: A total of 0 ns were simulated with a time step of 1 fs. 72: Neighbor searching was performed every 10 steps. 72: The Cut-off algorithm was used for electrostatic interactions. 72: with a cut-off of 1 nm. 72: A single cut-off of 1.1 nm was used for Van der Waals interactions. 72: [ OK ] ReportMethodsTest.ToolEndToEndTest (3 ms) 72: [----------] 4 tests from ReportMethodsTest (3 ms total) 72: 72: [----------] 4 tests from ConvertTprTest 72: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Setting the LD random seed to -897613834 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 200000 72: Runtime for the run 200 ps 72: Run end step 200000 72: Run end time 200 ps 72: 72: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (278 ms) 72: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Setting the LD random seed to -554699025 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime to 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (283 ms) 72: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Setting nsteps to 102 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Setting the LD random seed to 1855651581 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 102 72: Runtime for the run 0.102 ps 72: Run end step 102 72: Run end time 0.102 ps 72: 72: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (282 ms) 72: [ RUN ] ConvertTprTest.generateVelocitiesTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Setting the LD random seed to -44236805 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprTest.generateVelocitiesTest (271 ms) 72: [----------] 4 tests from ConvertTprTest (1118 ms total) 72: 72: [----------] 1 test from ConvertTprNoVelocityTest 72: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: 72: NOTE 3 [file lysozyme.top, line 1465]: 72: Zero-step energy minimization will alter the coordinates before 72: calculating the energy. If you just want the energy of a single point, 72: try zero-step MD (with unconstrained_start = yes). To do multiple 72: single-point energy evaluations of different configurations of the same 72: topology, use mdrun -rerun. 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 72: Setting the LD random seed to -1610616867 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (277 ms) 72: [----------] 1 test from ConvertTprNoVelocityTest (277 ms total) 72: 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: trr version: GMX_trn_file (single precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:86: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:123: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md (0 ms) 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats (7 ms total) 72: 72: [----------] 35 tests from Works/TrjconvDumpTest 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 (0 ms) 72: [----------] 35 tests from Works/TrjconvDumpTest (15 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 70 tests from 8 test suites ran. (2003 ms total) 72: [ PASSED ] 63 tests. 72: [ SKIPPED ] 7 tests, listed below: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72/104 Test #72: ToolUnitTests ............................. Passed 2.02 sec test 73 Start 73: ToolWithLeaksUnitTests 73: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests 73: Test timeout computed to be: 1920 73: [==========] Running 2 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 1 test from ConvertTprTest 73: [ RUN ] ConvertTprTest.selectIndexTest 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 73: Setting the LD random seed to -1091108889 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprTest.selectIndexTest (290 ms) 73: [----------] 1 test from ConvertTprTest (290 ms total) 73: 73: [----------] 1 test from ConvertTprNoVelocityTest 73: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: 73: NOTE 3 [file lysozyme.top, line 1465]: 73: Zero-step energy minimization will alter the coordinates before 73: calculating the energy. If you just want the energy of a single point, 73: try zero-step MD (with unconstrained_start = yes). To do multiple 73: single-point energy evaluations of different configurations of the same 73: topology, use mdrun -rerun. 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 73: Setting the LD random seed to -423649538 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (268 ms) 73: [----------] 1 test from ConvertTprNoVelocityTest (268 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 2 tests from 2 test suites ran. (559 ms total) 73: [ PASSED ] 2 tests. 73/104 Test #73: ToolWithLeaksUnitTests .................... Passed 0.57 sec test 74 Start 74: H5mdTests 74: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/h5md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/H5mdTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/h5md/tests 74: Test timeout computed to be: 30 74: [==========] Running 1 test from 1 test suite. 74: [----------] Global test environment set-up. 74: [----------] 1 test from H5mdDisabledTest 74: [ RUN ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled 74: [ OK ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled (0 ms) 74: [----------] 1 test from H5mdDisabledTest (0 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 1 test from 1 test suite ran. (0 ms total) 74: [ PASSED ] 1 test. 74/104 Test #74: H5mdTests ................................. Passed 0.01 sec test 75 Start 75: FileIOTests 75: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/FileIOTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/fileio/tests 75: Test timeout computed to be: 30 75: [==========] Running 432 tests from 17 test suites. 75: [----------] Global test environment set-up. 75: [----------] 4 tests from Checkpoint 75: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 75: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 75: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 75: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripInt64 75: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripReal 75: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 75: [----------] 4 tests from Checkpoint (0 ms total) 75: 75: [----------] 1 test from StructureIOTest 75: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 75: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 75: [----------] 1 test from StructureIOTest (0 ms total) 75: 75: [----------] 2 tests from FileMD5Test 75: [ RUN ] FileMD5Test.CanComputeMD5 75: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 75: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 75: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 75: [----------] 2 tests from FileMD5Test (1 ms total) 75: 75: [----------] 4 tests from FileTypeTest 75: [ RUN ] FileTypeTest.CorrectValueForEmptyString 75: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForNoExtension 75: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 75: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 75: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 75: [----------] 4 tests from FileTypeTest (0 ms total) 75: 75: [----------] 4 tests from ColorMapTest 75: [ RUN ] ColorMapTest.CanReadFromFile 75: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 75: [ RUN ] ColorMapTest.CanWriteToFile 75: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 75: [ RUN ] ColorMapTest.RoundTrip 75: [ OK ] ColorMapTest.RoundTrip (0 ms) 75: [ RUN ] ColorMapTest.SearchWorks 75: [ OK ] ColorMapTest.SearchWorks (0 ms) 75: [----------] 4 tests from ColorMapTest (0 ms total) 75: 75: [----------] 4 tests from MatioTest 75: [ RUN ] MatioTest.CanWriteToFile 75: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 75: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanConvertToNewRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 75: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) 75: [----------] 4 tests from MatioTest (1 ms total) 75: 75: [----------] 3 tests from MrcSerializer 75: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 75: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 75: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 75: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 75: [----------] 3 tests from MrcSerializer (0 ms total) 75: 75: [----------] 4 tests from MrcDensityMap 75: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 75: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 75: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 75: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 75: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 75: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 75: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 75: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 75: [----------] 4 tests from MrcDensityMap (0 ms total) 75: 75: [----------] 8 tests from MrcDensityMapHeaderTest 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 75: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.IsSane 75: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 75: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 75: 75: [----------] 10 tests from ReadTest 75: [ RUN ] ReadTest.get_eint_ReadsInteger 75: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_eint64_ReadsInteger 75: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsInteger 75: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsFloat 75: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 75: [ RUN ] ReadTest.get_ereal_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not a 75: real value 75: 75: 75: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 75: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 75: [----------] 10 tests from ReadTest (0 ms total) 75: 75: [----------] 3 tests from TimeControlTest 75: [ RUN ] TimeControlTest.UnSetHasNoValue 75: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 75: [ RUN ] TimeControlTest.CanSetValue 75: [ OK ] TimeControlTest.CanSetValue (0 ms) 75: [ RUN ] TimeControlTest.CanUnsetValueAgain 75: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 75: [----------] 3 tests from TimeControlTest (0 ms total) 75: 75: [----------] 1 test from TngTest 75: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 75: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 75: [----------] 1 test from TngTest (0 ms total) 75: 75: [----------] 4 tests from XvgioTest 75: [ RUN ] XvgioTest.readXvgIntWorks 75: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgRealWorks 75: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 75: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgDeprecatedWorks 75: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 75: [----------] 4 tests from XvgioTest (0 ms total) 75: 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 75: 75: [----------] 370 tests from FileTypeMatch/FileTypeTest 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 (0 ms) 75: [----------] 370 tests from FileTypeMatch/FileTypeTest (1 ms total) 75: 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 (0 ms) 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 (0 ms) 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest (0 ms total) 75: 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 432 tests from 17 test suites ran. (8 ms total) 75: [ PASSED ] 432 tests. 75/104 Test #75: FileIOTests ............................... Passed 0.02 sec test 76 Start 76: SelectionUnitTests 76: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/gromacs/selection/tests 76: Test timeout computed to be: 30 76: [==========] Running 201 tests from 11 test suites. 76: [----------] Global test environment set-up. 76: [----------] 1 test from IndexGroupTest 76: [ RUN ] IndexGroupTest.RemovesDuplicates 76: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 76: [----------] 1 test from IndexGroupTest (0 ms total) 76: 76: [----------] 15 tests from IndexBlockTest 76: [ RUN ] IndexBlockTest.CreatesUnknownBlock 76: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 76: [ RUN ] IndexBlockTest.CreatesAtomBlock 76: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesSingleBlock 76: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 76: [----------] 15 tests from IndexBlockTest (0 ms total) 76: 76: [----------] 11 tests from IndexMapTest 76: [ RUN ] IndexMapTest.InitializesAtomBlock 76: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 76: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 76: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 76: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 76: [ RUN ] IndexMapTest.InitializesMoleculeBlock 76: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsSingleBlock 76: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocks 76: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 76: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 76: [ RUN ] IndexMapTest.HandlesMultipleRequests 76: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 76: [----------] 11 tests from IndexMapTest (1 ms total) 76: 76: [----------] 3 tests from IndexGroupsAndNamesTest 76: [ RUN ] IndexGroupsAndNamesTest.containsNames 76: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 76: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 76: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 76: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 76: 76: [----------] 15 tests from NeighborhoodSearchTest 76: [ RUN ] NeighborhoodSearchTest.SimpleSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSearch (10 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 76: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (10 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchBox 76: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 76: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (5 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 76: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 76: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 76: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (25 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 76: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 76: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 76: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 76: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 76: [----------] 15 tests from NeighborhoodSearchTest (61 ms total) 76: 76: [----------] 13 tests from PositionCalculationTest 76: [ RUN ] PositionCalculationTest.ComputesAtomPositions 76: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 76: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionMask 76: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 76: [----------] 13 tests from PositionCalculationTest (1 ms total) 76: 76: [----------] 33 tests from SelectionCollectionTest 76: [ RUN ] SelectionCollectionTest.HandlesNoSelections 76: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 76: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 76: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 76: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 76: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 76: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 76: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 76: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 76: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 76: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 76: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 76: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 76: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 76: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 76: [----------] 33 tests from SelectionCollectionTest (5 ms total) 76: 76: [----------] 14 tests from SelectionCollectionInteractiveTest 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 76: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 76: [----------] 14 tests from SelectionCollectionInteractiveTest (2 ms total) 76: 76: [----------] 70 tests from SelectionCollectionDataTest 76: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 76: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 76: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResnr 76: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 76: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 76: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 76: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesChain 76: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMass 76: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCharge 76: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 76: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 76: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 76: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBeta 76: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResname 76: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 76: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 76: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 76: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 76: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 76: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 76: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 76: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 76: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 76: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 76: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 76: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 76: [----------] 70 tests from SelectionCollectionDataTest (29 ms total) 76: 76: [----------] 17 tests from SelectionOptionTest 76: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 76: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 76: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 76: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 76: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptySelections 76: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 76: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelections 76: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 76: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesAdjuster 76: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 76: [----------] 17 tests from SelectionOptionTest (2 ms total) 76: 76: [----------] 9 tests from SelectionFileOptionTest 76: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 76: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 76: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 76: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 201 tests from 11 test suites ran. (107 ms total) 76: [ PASSED ] 201 tests. 76/104 Test #76: SelectionUnitTests ........................ Passed 0.12 sec test 77 Start 77: MdrunOutputTests 77: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 12 tests from 5 test suites. 77: [----------] Global test environment set-up. 77: [----------] 1 test from MdrunTest 77: [ RUN ] MdrunTest.WritesHelp 77: [ OK ] MdrunTest.WritesHelp (15 ms) 77: [----------] 1 test from MdrunTest (15 ms total) 77: 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -1904303109 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.297 0.149 199.9 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 1.162 20.651 74.343 0.000 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (154 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -1543786538 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.014 0.007 199.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 23.911 1.004 3.613 0.002 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (11 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -35651922 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.007 198.5 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 23.338 1.028 3.702 0.002 77: Reading frame 0 time 0.000 77: # Atoms 3 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (11 ms) 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (176 ms total) 77: 77: [----------] 2 tests from Argon12/OutputFiles 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.017 0.008 199.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 173.430 0.138 0.498 0.024 77: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (12 ms) 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.016 0.008 199.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 178.687 0.134 0.484 0.025 77: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (11 ms) 77: [----------] 2 tests from Argon12/OutputFiles (23 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/Trajectories 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -1620206090 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.010 199.0 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 58.473 0.410 1.478 0.004 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (15 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to 1862269894 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.018 0.009 199.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 66.141 0.363 1.306 0.005 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (14 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -443617378 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.014 0.007 198.9 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 88.492 0.271 0.976 0.006 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (12 ms) 77: [----------] 3 tests from MdrunCanWrite/Trajectories (42 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to 2137972717 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.005 198.7 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 48.879 0.491 1.768 0.003 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (10 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 77: 77: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: The Berendsen barostat does not generate any strictly correct ensemble, 77: and should not be used for new production simulations (in our opinion). 77: We recommend using the C-rescale barostat instead. 77: 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: 77: There was 1 WARNING 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -1197474439 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.006 198.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 45.781 0.524 1.887 0.003 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (10 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -890520129 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.010 0.005 198.7 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 49.649 0.483 1.740 0.003 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (9 ms) 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories (30 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 12 tests from 5 test suites ran. (337 ms total) 77: [ PASSED ] 12 tests. 77/104 Test #77: MdrunOutputTests .......................... Passed 0.35 sec test 78 Start 78: MdrunModulesTests 78: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 15 tests from 3 test suites. 78: [----------] Global test environment set-up. 78: [----------] 9 tests from DensityFittingTest 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.85652562592421e+03 78: Maximum force = 4.50998690851897e+03 on atom 3 78: Norm of force = 1.68168494163492e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2146695969 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (8 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -9.82077921283928e+03 78: Maximum force = 7.39548334240075e+03 on atom 2 78: Norm of force = 2.78250777177324e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -706744457 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (6 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (5 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Overriding nsteps with value passed on the command line: 4 steps 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 4 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 5 steps. 78: Potential Energy = -5.47393359520241e+03 78: Maximum force = 6.13219949575544e+03 on atom 2 78: Norm of force = 1.77021426574818e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 2113273854 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (6 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (4 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.85652562592421e+03 78: Maximum force = 4.50998690851897e+03 on atom 3 78: Norm of force = 1.68168494163492e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1109839875 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (4 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -2.71386626041483e+04 78: Maximum force = 6.78276504921089e+03 on atom 2 78: Norm of force = 1.96088640980697e+03 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -110653 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (3 ms) 78: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: Setting the LD random seed to -524555265 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 78: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (4 ms) 78: [ RUN ] DensityFittingTest.CheckpointWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (2) 78: 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -226828293 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.014 0.007 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 35.989 0.667 2.401 0.005 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 78: Can not increase nstlist because an NVE ensemble is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.010 0.005 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 84.984 0.282 1.017 0.012 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (17 ms) 78: [----------] 9 tests from DensityFittingTest (60 ms total) 78: 78: [----------] 4 tests from MimicTest 78: [ RUN ] MimicTest.OneQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 28 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 185.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 514.755 0.047 0.168 0.071 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -16812873 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.OneQuantumMol (4 ms) 78: [ RUN ] MimicTest.AllQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 20 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 183.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 671.089 0.036 0.129 0.093 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -3674115 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.AllQuantumMol (3 ms) 78: [ RUN ] MimicTest.TwoQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 21 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 183.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 735.067 0.033 0.118 0.102 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2097149943 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.TwoQuantumMol (3 ms) 78: [ RUN ] MimicTest.BondCuts 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 66.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: NVE simulation: will use the initial temperature of 300.368 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 78: 78: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 16 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 190.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 356.330 0.067 0.242 0.095 78: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -152211633 78: 78: Generated 2211 of the 2211 non-bonded parameter combinations 78: 78: Generated 2211 of the 2211 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.BondCuts (11 ms) 78: [----------] 4 tests from MimicTest (23 ms total) 78: 78: [----------] 2 tests from WithIntegrator/ImdTest 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 78: Generating 1-4 interactions: fudge = 1 78: 78: NOTE 1 [file glycine_vacuo.top, line 12]: 78: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 78: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 78: the time step of 2.0e-03 ps. 78: Maybe you forgot to change the constraints mdp option. 78: 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 52817. 78: IMD: -imdwait not set, starting simulation. 78: starting mdrun 'Glycine' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -1468153861 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.017 0.009 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 59.972 0.400 2.881 0.003 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (70 ms) 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 78: apply to steep. 78: 78: Generating 1-4 interactions: fudge = 1 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 36277. 78: IMD: -imdwait not set, starting simulation. 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = 1.19770464690297e+03 78: Maximum force = 1.77948604657897e+04 on atom 9 78: Norm of force = 7.87328617833981e+03 78: Setting the LD random seed to 1006464927 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (58 ms) 78: [----------] 2 tests from WithIntegrator/ImdTest (129 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 15 tests from 3 test suites ran. (253 ms total) 78: [ PASSED ] 15 tests. 78/104 Test #78: MdrunModulesTests ......................... Passed 0.26 sec test 79 Start 79: MdrunIOTests 79: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 76 tests from 13 test suites. 79: [----------] Global test environment set-up. 79: [----------] 9 tests from GromppTest 79: [ RUN ] GromppTest.EmptyMdpFileWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -1454559937 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group rest: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -1485309958 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group Methanol: Single, 3 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 3.0 280.0 79: 6.0- 270.0 79: Simulated annealing for group SOL: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group Methanol is 7.20 79: Number of degrees of freedom in T-Coupling group SOL is 4.80 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to 2132266749 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 79: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 79: Setting the LD random seed to -613096469 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (4 ms) 79: [ RUN ] GromppTest.HandlesMaxwarn 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: The Berendsen thermostat does not generate the correct kinetic energy 79: distribution, and should not be used for new production simulations (in 79: our opinion). We would recommend the V-rescale thermostat. 79: 79: Number of degrees of freedom in T-Coupling group System is 12.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Setting the LD random seed to 932572415 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 79: [ RUN ] GromppTest.MaxwarnShouldBePositive 79: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 79: [ RUN ] GromppTest.ValidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: 0.613 nm 0.000 nm 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -151259669 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 79: [ RUN ] GromppTest.InvalidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: Setting the LD random seed to -1346656769 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) 79: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 79: Setting the LD random seed to -294933765 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (4 ms) 79: [----------] 9 tests from GromppTest (28 ms total) 79: 79: [----------] 6 tests from MdrunTerminationTest 79: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -205523973 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 33.590 0.715 2.572 0.002 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.006 0.003 197.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 83.957 0.286 1.029 0.006 79: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (17 ms) 79: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 1, rlist from 1.035 to 1 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 9: Run time exceeded 0.000 hours, will terminate the run within 200 steps 79: Setting the LD random seed to -1781017605 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 18 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 1023.866 0.023 0.084 0.071 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 102 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 100 79: Runtime for the run 0.1 ps 79: Run end step 100 79: Run end time 0.1 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 102 79: Runtime for the run 0.102 ps 79: Run end step 102 79: Run end time 0.102 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 67.990 0.353 1.271 0.005 79: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (20 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -136512770 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.415 0.208 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 1.248 19.227 69.217 0.000 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 44.246 0.542 1.953 0.003 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 6 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 34.378 0.698 2.513 0.002 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 8 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 8 79: Runtime for the run 0.008 ps 79: Run end step 8 79: Run end time 0.008 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 51.733 0.464 1.670 0.004 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: NOTE: 28 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.000 172.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 852.677 0.028 0.101 0.059 79: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (238 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -436739074 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 51.750 0.464 1.670 0.004 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.406 0.203 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 2.127 11.283 40.618 0.000 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (214 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -814823020 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 50.651 0.474 1.706 0.004 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 4 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (9 ms) 79: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to 2147483135 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 45.479 0.528 1.900 0.003 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Setting nsteps to 4 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 49.394 0.486 1.749 0.003 79: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (16 ms) 79: [----------] 6 tests from MdrunTerminationTest (517 ms total) 79: 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.009 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 157.319 0.153 0.549 0.011 79: trr version: GMX_trn_file (double precision) 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: 79: Dumping frame at t= 0.016 ps 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Last frame -1 time 0.016 79: 79: There were 3 NOTEs 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: Analysing residue names: 79: There are: 2 Water residues 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: Reading Coordinates, Velocities and Box size from old trajectory 79: 79: Will read whole trajectory 79: 79: Using frame at t = 0.016 ps 79: 79: Starting time for run is 0 ps 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (19 ms) 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 180.292 0.133 0.479 0.013 79: 79: 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (13 ms) 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (33 ms total) 79: 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 197.202 0.122 0.438 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 115.162 0.208 0.750 0.016 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 115.619 0.208 0.747 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 184.786 0.130 0.468 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.341 0.222 0.797 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 102.624 0.234 0.842 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (31 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 138.824 0.173 0.622 0.019 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 87.236 0.275 0.990 0.012 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.102 0.245 0.881 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (37 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 170.668 0.141 0.506 0.024 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.344 0.244 0.879 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 90.091 0.266 0.959 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (39 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 193.098 0.124 0.447 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.006 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 119.710 0.200 0.722 0.017 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 114.226 0.210 0.756 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 201.795 0.119 0.428 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.608 0.232 0.834 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 117.101 0.205 0.738 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 198.166 0.121 0.436 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 110.518 0.217 0.782 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.344 0.216 0.776 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (29 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 197.715 0.121 0.437 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.402 0.223 0.804 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 96.973 0.247 0.891 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (36 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 201.907 0.119 0.428 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.750 0.231 0.833 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.481 0.215 0.775 0.008 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 197.139 0.122 0.438 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 109.652 0.219 0.788 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.381 0.230 0.828 0.007 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 207.462 0.116 0.416 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.603 0.215 0.774 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.245 0.216 0.777 0.008 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (29 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 182.315 0.132 0.474 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.456 0.223 0.804 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.413 0.244 0.878 0.007 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (31 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 191.026 0.126 0.452 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.323 0.237 0.853 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.294 0.222 0.798 0.008 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (31 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 187.423 0.128 0.461 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 99.688 0.241 0.867 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.655 0.236 0.850 0.007 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (35 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 206.247 0.116 0.419 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.323 0.254 0.916 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.361 0.254 0.916 0.007 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (33 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 193.074 0.124 0.447 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 102.601 0.234 0.842 0.007 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.075 0.222 0.799 0.008 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 178.145 0.135 0.485 0.060 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 88.167 0.272 0.980 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.566 0.251 0.904 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (54 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 170.413 0.141 0.507 0.057 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.396 0.252 0.906 0.032 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 90.655 0.265 0.953 0.030 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (48 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 163.009 0.147 0.530 0.055 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 89.952 0.267 0.961 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.937 0.245 0.882 0.033 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (59 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 147.594 0.163 0.585 0.050 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 85.143 0.282 1.015 0.029 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 90.529 0.265 0.954 0.030 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (57 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 157.536 0.152 0.548 0.053 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 87.809 0.273 0.984 0.029 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 85.996 0.279 1.005 0.029 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (79 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 152.528 0.157 0.566 0.051 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 88.903 0.270 0.972 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 82.081 0.292 1.053 0.028 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (157 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 143.815 0.167 0.601 0.048 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 92.827 0.259 0.931 0.031 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.013 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 61.796 0.388 1.398 0.021 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (72 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.009 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 156.000 0.154 0.554 0.052 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.861 0.236 0.848 0.034 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 92.428 0.260 0.935 0.031 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (86 ms) 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1137 ms total) 79: 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.013 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.341 0.216 0.776 0.046 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 79.299 0.303 1.090 0.033 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 78.533 0.306 1.100 0.033 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (55 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 132.697 0.181 0.651 0.055 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 77.520 0.310 1.115 0.032 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 78.411 0.306 1.102 0.033 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (52 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 133.456 0.180 0.647 0.056 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 73.333 0.327 1.178 0.031 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 70.173 0.342 1.231 0.029 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (55 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 127.122 0.189 0.680 0.053 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.010 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 75.048 0.320 1.151 0.031 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 80.734 0.297 1.070 0.034 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (53 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 125.261 0.192 0.690 0.052 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 73.345 0.327 1.178 0.031 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 69.627 0.345 1.241 0.029 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (72 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 131.921 0.182 0.655 0.055 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 70.198 0.342 1.231 0.029 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 67.589 0.355 1.278 0.028 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (187 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 123.269 0.195 0.701 0.051 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.010 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 74.805 0.321 1.155 0.031 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 77.069 0.311 1.121 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (74 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 126.061 0.190 0.685 0.053 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 72.808 0.330 1.187 0.030 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.331 0.314 1.132 0.032 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (78 ms) 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (630 ms total) 79: 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 196.774 0.122 0.439 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 84.650 0.284 1.021 0.012 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.882 0.227 0.816 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (35 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 184.836 0.130 0.467 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 96.272 0.249 0.897 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.401 0.230 0.828 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (32 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 192.146 0.125 0.450 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.016 0.229 0.823 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.941 0.224 0.808 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (30 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 191.883 0.125 0.450 0.027 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 99.767 0.241 0.866 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.640 0.225 0.810 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (32 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 182.666 0.131 0.473 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 78.149 0.307 1.106 0.011 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.018 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 44.234 0.543 1.953 0.006 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (45 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 175.401 0.137 0.493 0.024 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 89.466 0.268 0.966 0.012 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.091 0.228 0.822 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (34 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 165.478 0.145 0.522 0.023 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 96.866 0.248 0.892 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 98.217 0.244 0.880 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (35 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 142.884 0.168 0.605 0.020 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 93.265 0.257 0.926 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.955 0.229 0.823 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (38 ms) 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (284 ms total) 79: 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 168.015 0.143 0.514 0.023 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.626 0.246 0.885 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.562 0.230 0.826 0.015 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (33 ms) 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 159.713 0.150 0.541 0.022 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.129 0.255 0.918 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.604 0.313 1.128 0.011 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (36 ms) 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (70 ms total) 79: 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 183.586 0.131 0.471 0.025 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.071 0.252 0.909 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.009 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 83.660 0.287 1.033 0.012 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (34 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 185.393 0.129 0.466 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.989 0.235 0.847 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.811 0.250 0.902 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (32 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 199.546 0.120 0.433 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.800 0.227 0.817 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 93.098 0.258 0.928 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (31 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 189.685 0.127 0.455 0.026 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.428 0.246 0.887 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.279 0.255 0.916 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (32 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 146.499 0.164 0.590 0.020 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.026 0.255 0.919 0.013 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 102.427 0.234 0.844 0.014 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (34 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 176.289 0.136 0.490 0.024 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 99.914 0.240 0.865 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.011 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 67.740 0.354 1.275 0.009 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (36 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 164.828 0.146 0.524 0.023 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.014 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 57.536 0.417 1.502 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.878 0.250 0.901 0.013 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (39 ms) 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (241 ms total) 79: 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 79: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 173.416 0.138 0.498 0.024 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 102.511 0.234 0.843 0.014 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 87.656 0.274 0.986 0.012 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (34 ms) 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (34 ms total) 79: 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 121.487 0.198 0.711 0.008 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.013 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 58.236 0.412 1.484 0.004 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.011 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 67.860 0.354 1.273 0.005 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (47 ms) 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 124.311 0.193 0.695 0.009 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 66.599 0.360 1.297 0.005 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 70.843 0.339 1.220 0.005 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (44 ms) 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (91 ms total) 79: 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Setting the AWH bias MC random seed to 1976748863 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -176562369 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.013 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 115.087 0.209 0.751 0.029 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.013 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 58.718 0.409 1.471 0.015 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 64.753 0.371 1.334 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (68 ms) 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: Setting the AWH bias MC random seed to -540025090 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -33595701 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.013 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.755 0.215 0.773 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 65.421 0.367 1.321 0.017 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.012 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 62.306 0.385 1.387 0.016 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (66 ms) 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (134 ms total) 79: 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 79: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 122.334 0.196 0.706 0.051 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 67.092 0.358 1.288 0.028 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 71.680 0.335 1.205 0.030 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (69 ms) 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (69 ms total) 79: 79: [----------] 3 tests from Checking/InitialConstraintsTest 79: [ RUN ] Checking/InitialConstraintsTest.Works/0 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to -1090852098 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 28.380 0.846 3.044 0.002 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (10 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/1 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to -537133331 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 29.222 0.821 2.957 0.002 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (10 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: Integrator method md-vv-avek is implemented primarily for validation 79: purposes; for molecular dynamics, you should probably be using md or 79: md-vv 79: 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to 2112746431 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 34.294 0.700 2.519 0.002 79: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (9 ms) 79: [----------] 3 tests from Checking/InitialConstraintsTest (29 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 76 tests from 13 test suites ran. (3466 ms total) 79: [ PASSED ] 76 tests. 79/104 Test #79: MdrunIOTests .............................. Passed 3.48 sec test 80 Start 80: MdrunTestsOneRank 80: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 31 tests from 9 test suites. 80: [----------] Global test environment set-up. 80: [----------] 2 tests from AwhTest 80: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.015 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 117.261 0.205 0.737 0.030 80: [ OK ] AwhTest.SingleBiasMultiDimCanRun (34 ms) 80: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 120.738 0.199 0.716 0.031 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.010 198.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 190.339 0.126 0.454 0.048 80: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (45 ms) 80: [----------] 2 tests from AwhTest (79 ms total) 80: 80: [----------] 1 test from CompelTest 80: [ RUN ] CompelTest.SwapCanRun 80: Generating 1-4 interactions: fudge = 0.5 80: Split0 group 'Ch0' contains 83 atoms. 80: Split1 group 'Ch1' contains 83 atoms. 80: Solvent group 'SOL' contains 11931 atoms. 80: Swap group 'NA+' contains 19 atoms. 80: Swap group 'CL-' contains 19 atoms. 80: Number of degrees of freedom in T-Coupling group System is 27869.00 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Determining initial numbers of ions per compartment. 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 2 steps, 0.0 ps. 80: Setting the LD random seed to -276889937 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning all bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.249 0.125 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 8.306 2.889 41.607 0.332 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 80: 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Copying channel fluxes from checkpoint file data 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: NOTE: 19 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.181 0.091 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 11.444 2.097 30.199 0.458 80: [ OK ] CompelTest.SwapCanRun (581 ms) 80: [----------] 1 test from CompelTest (581 ms total) 80: 80: [----------] 6 tests from BondedInteractionsTest 80: [ RUN ] BondedInteractionsTest.NormalBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 20 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 186.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 549.073 0.044 0.157 0.025 80: Setting the LD random seed to 1602093039 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalBondWorks (3 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 16 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 185.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 543.310 0.044 0.159 0.025 80: Setting the LD random seed to -23462242 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedBondWorks (3 ms) 80: [ RUN ] BondedInteractionsTest.NormalAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 18 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 185.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 604.988 0.040 0.143 0.028 80: Setting the LD random seed to -1214812515 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalAngleWorks (3 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 24 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 184.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 619.466 0.039 0.139 0.029 80: Setting the LD random seed to -152143115 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (3 ms) 80: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 15 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 191.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 354.240 0.068 0.244 0.016 80: Setting the LD random seed to -86509697 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalDihedralWorks (3 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 24 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 185.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 463.412 0.052 0.186 0.021 80: Setting the LD random seed to -9969697 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (3 ms) 80: [----------] 6 tests from BondedInteractionsTest (21 ms total) 80: 80: [----------] 2 tests from BoxDeformationTest 80: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 25 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 161.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1654.739 0.015 0.104 0.115 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -816185345 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Setting gen_seed to -1478688785 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (3 ms) 80: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group rest is 1293.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 20 steps, 0.0 ps. 80: Setting the LD random seed to -1090552065 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 80: 80: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 80: 80: Estimate for the relative computational load of the PME mesh part: 0.15 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.059 0.030 199.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 121.939 0.197 1.417 0.457 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (303 ms) 80: [----------] 2 tests from BoxDeformationTest (306 ms total) 80: 80: [----------] 1 test from PositionRestraintCommTest 80: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any of the VCM groups 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any center of mass motion removal group. 80: This may lead to artifacts. 80: In most cases one should use one group for the whole system. 80: 80: Number of degrees of freedom in T-Coupling group System is 29527.73 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Channel_coco in octane membrane' 80: 10 steps, 0.0 ps. 80: Setting the LD random seed to -548 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.314 0.157 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 12.106 1.983 14.274 0.968 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (484 ms) 80: [----------] 1 test from PositionRestraintCommTest (484 ms total) 80: 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -50472381 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 36.405 0.659 2.373 0.010 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1236266393 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.009 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 46.265 0.519 1.867 0.012 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 80: 80: 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (366 ms) 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -200961 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 48.932 0.490 1.766 0.013 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -542130433 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 54.475 0.441 1.586 0.015 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (39 ms) 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (405 ms total) 80: 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -54341 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 199.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 36.277 0.662 2.382 0.003 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -95249 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.023 0.012 199.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 37.437 0.641 2.308 0.003 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (32 ms) 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (32 ms total) 80: 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 102.040 0.235 0.847 0.026 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (16 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 95.157 0.252 0.908 0.024 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (17 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 99.405 0.241 0.869 0.025 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (16 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 103.205 0.233 0.837 0.026 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (16 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 100.499 0.239 0.860 0.026 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (16 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 80: Parrinello-Rahman is not implemented in md-vv. 80: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 110.507 0.217 0.782 0.028 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (19 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.008 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 92.775 0.259 0.931 0.024 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (20 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 97.755 0.246 0.884 0.025 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (19 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 97.088 0.247 0.890 0.025 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (40 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 83.886 0.286 1.030 0.021 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (39 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 73.206 0.328 1.180 0.019 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (40 ms) 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest (264 ms total) 80: 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -1614349620 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 197.912 0.121 0.873 0.007 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (12 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -537002018 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 199.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 177.159 0.135 0.975 0.006 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (12 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -35960193 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.010 199.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 161.528 0.149 1.070 0.006 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (13 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -1208492822 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 199.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 203.240 0.118 0.850 0.007 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (11 ms) 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (50 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 31 tests from 9 test suites ran. (2338 ms total) 80: [ PASSED ] 30 tests. 80: [ SKIPPED ] 1 test, listed below: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80/104 Test #80: MdrunTestsOneRank ......................... Passed 2.35 sec test 81 Start 81: MdrunTestsTwoRanks 81: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 31 tests from 9 test suites. 81: [----------] Global test environment set-up. 81: [----------] 2 tests from AwhTest 81: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 11.1%. 81: The balanceable part of the MD step is 59%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 6.5%. 81: 81: NOTE: 6.5 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.070 0.018 396.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 103.209 0.233 0.837 0.026 81: [ OK ] AwhTest.SingleBiasMultiDimCanRun (36 ms) 81: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 13.7%. 81: The balanceable part of the MD step is 58%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.0%. 81: 81: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.056 0.014 397.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 128.347 0.187 0.673 0.033 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 13.9%. 81: The balanceable part of the MD step is 63%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.7%. 81: 81: NOTE: 8.7 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 42 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.009 395.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 206.744 0.116 0.418 0.053 81: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (47 ms) 81: [----------] 2 tests from AwhTest (84 ms total) 81: 81: [----------] 1 test from CompelTest 81: [ RUN ] CompelTest.SwapCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Split0 group 'Ch0' contains 83 atoms. 81: Split1 group 'Ch1' contains 83 atoms. 81: Solvent group 'SOL' contains 11931 atoms. 81: Swap group 'NA+' contains 19 atoms. 81: Swap group 'CL-' contains 19 atoms. 81: Number of degrees of freedom in T-Coupling group System is 27869.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Determining initial numbers of ions per compartment. 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 2 steps, 0.0 ps. 81: Setting the LD random seed to -151191778 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning all bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.2%. 81: The balanceable part of the MD step is 27%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.3%. 81: 81: 81: NOTE: 4 % of the run time was spent in domain decomposition, 81: 25 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.409 0.102 399.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 10.128 2.370 34.122 0.405 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 81: 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Copying channel fluxes from checkpoint file data 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: NOTE: 14 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.299 0.075 399.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 13.843 1.734 24.965 0.554 81: [ OK ] CompelTest.SwapCanRun (554 ms) 81: [----------] 1 test from CompelTest (554 ms total) 81: 81: [----------] 6 tests from BondedInteractionsTest 81: [ RUN ] BondedInteractionsTest.NormalBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 24 % of the run time was spent in domain decomposition, 81: 15 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 382.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 259.869 0.092 0.332 0.012 81: Setting the LD random seed to -278793 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalBondWorks (5 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 23 % of the run time was spent in domain decomposition, 81: 15 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 5 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 380.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 332.771 0.072 0.260 0.015 81: Setting the LD random seed to -377494533 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedBondWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.NormalAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 29 % of the run time was spent in domain decomposition, 81: 15 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 382.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 273.914 0.088 0.315 0.013 81: Setting the LD random seed to 736098223 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalAngleWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 32 % of the run time was spent in domain decomposition, 81: 16 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 384.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 252.711 0.095 0.342 0.012 81: Setting the LD random seed to 2113923711 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 24 % of the run time was spent in domain decomposition, 81: 14 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 380.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 308.415 0.078 0.280 0.014 81: Setting the LD random seed to 503185263 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalDihedralWorks (4 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 25 % of the run time was spent in domain decomposition, 81: 15 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 380.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 337.262 0.071 0.256 0.016 81: Setting the LD random seed to -807415947 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (4 ms) 81: [----------] 6 tests from BondedInteractionsTest (28 ms total) 81: 81: [----------] 2 tests from BoxDeformationTest 81: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 25 % of the run time was spent in domain decomposition, 81: 21 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.000 321.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 812.074 0.030 0.213 0.056 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 267910646 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Setting gen_seed to -717752921 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (4 ms) 81: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group rest is 1293.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 20 steps, 0.0 ps. 81: Setting the LD random seed to 2059205375 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 81: 81: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 81: 81: Estimate for the relative computational load of the PME mesh part: 0.15 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB got disabled because it was unsuitable to use. 81: Average load imbalance: 14.1%. 81: The balanceable part of the MD step is 53%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.5%. 81: 81: NOTE: 7.5 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: You can consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.121 0.030 399.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 120.065 0.200 1.439 0.450 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (317 ms) 81: [----------] 2 tests from BoxDeformationTest (322 ms total) 81: 81: [----------] 1 test from PositionRestraintCommTest 81: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any of the VCM groups 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any center of mass motion removal group. 81: This may lead to artifacts. 81: In most cases one should use one group for the whole system. 81: 81: Number of degrees of freedom in T-Coupling group System is 29527.73 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Channel_coco in octane membrane' 81: 10 steps, 0.0 ps. 81: Setting the LD random seed to -101548609 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 15 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.401 0.100 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 18.944 1.267 9.122 1.515 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (434 ms) 81: [----------] 1 test from PositionRestraintCommTest (434 ms total) 81: 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to 1572863997 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 44 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.049 0.012 397.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 34.740 0.691 2.487 0.009 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to 1055751167 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 397.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 47.526 0.505 1.818 0.013 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 81: 81: 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (363 ms) 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -119540994 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 40 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.040 0.010 396.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 42.955 0.559 2.011 0.011 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -4200489 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.042 0.011 397.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 40.612 0.591 2.127 0.011 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (49 ms) 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (413 ms total) 81: 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -33574314 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 49 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.051 0.013 398.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 33.994 0.706 2.542 0.002 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -1145583745 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 48 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.055 0.014 397.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 31.509 0.762 2.742 0.002 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (38 ms) 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (38 ms total) 81: 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 4.3%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.9%. 81: 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.042 0.011 396.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 73.078 0.328 1.182 0.019 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (21 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 15.6%. 81: The balanceable part of the MD step is 40%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 6.3%. 81: 81: NOTE: 6.3 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.039 0.010 397.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 79.353 0.302 1.089 0.020 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (23 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 14.8%. 81: The balanceable part of the MD step is 45%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 6.7%. 81: 81: NOTE: 6.7 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.009 396.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 88.934 0.270 0.972 0.023 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (19 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 16.0%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.1%. 81: 81: NOTE: 7.1 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 396.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 86.132 0.279 1.003 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (20 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 4.0%. 81: The balanceable part of the MD step is 53%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.2%. 81: 81: 81: NOTE: 44 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.009 397.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 87.968 0.273 0.982 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (19 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 81: Parrinello-Rahman is not implemented in md-vv. 81: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.037 0.009 397.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 83.549 0.287 1.034 0.021 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (23 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.039 0.010 397.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 80.299 0.299 1.076 0.020 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (23 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.009 398.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 88.027 0.273 0.982 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (22 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 398.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 87.001 0.276 0.993 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (40 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.009 397.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 88.052 0.273 0.981 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (40 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.009 398.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 85.814 0.280 1.007 0.022 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (40 ms) 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest (295 ms total) 81: 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -1090572481 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.4%. 81: The balanceable part of the MD step is 41%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.2%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.033 0.008 398.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 186.798 0.128 0.925 0.006 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (13 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -50612233 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.2%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.008 397.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 207.220 0.116 0.834 0.007 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (11 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -234959121 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.1%. 81: The balanceable part of the MD step is 49%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.0%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.032 0.008 397.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 191.762 0.125 0.901 0.007 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (12 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -34750499 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 3.5%. 81: The balanceable part of the MD step is 48%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.7%. 81: 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.009 397.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 178.436 0.135 0.968 0.006 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (13 ms) 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (51 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 31 tests from 9 test suites ran. (2340 ms total) 81: [ PASSED ] 30 tests. 81: [ SKIPPED ] 1 test, listed below: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81/104 Test #81: MdrunTestsTwoRanks ........................ Passed 2.35 sec test 82 Start 82: MdrunSingleRankAlgorithmsTests 82: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 82: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 600 82: [==========] Running 5 tests from 3 test suites. 82: [----------] Global test environment set-up. 82: [----------] 1 test from DispersionCorrectionTest 82: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 30.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: There are 9 non-linear virtual site constructions. Their contribution to 82: the energy error is approximated. In most cases this does not affect the 82: error significantly. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 82: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 82: 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Alanine dipeptide in vacuo' 82: 200 steps, 0.4 ps. 82: Setting the LD random seed to -67158274 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Converted 3 Bonds with virtual sites to connections, 7 left 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 12 Constraints with virtual sites to connections, 0 left 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.016 199.4 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 2117.779 0.011 0.082 0.355 82: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (45 ms) 82: [----------] 1 test from DispersionCorrectionTest (45 ms total) 82: 82: [----------] 1 test from OriresTest 82: [ RUN ] OriresTest.OriresCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 518.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There was 1 NOTE 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 82: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 82: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 82: 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 82: 10 steps, 0.0 ps. 82: Setting the LD random seed to -21497985 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 82: 82: turning H bonds into constraints... 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/orires_1lvz.gro' 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.009 199.0 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 211.630 0.113 0.817 0.263 82: [ OK ] OriresTest.OriresCanRun (337 ms) 82: [----------] 1 test from OriresTest (337 ms total) 82: 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 82: Number of degrees of freedom in T-Coupling group rest is 10.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to -537002258 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: Searching the wall atom type(s) 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.019 199.5 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 244.995 0.098 0.882 0.005 82: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 82: 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (559 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 82: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 82: The supported numbers are > 1. 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 all molecules should be neutral. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 you can only use domain decomposition when there 82: are only small molecules with all bonds constrained (mdrun will check for 82: this). 82: 82: Number of degrees of freedom in T-Coupling group rest is 9.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to -293650572 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.012 199.2 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 373.251 0.064 0.579 0.007 82: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (204 ms) 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (763 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 5 tests from 3 test suites ran. (1185 ms total) 82: [ PASSED ] 5 tests. 82/104 Test #82: MdrunSingleRankAlgorithmsTests ............ Passed 1.20 sec test 83 Start 83: Minimize1RankTests 83: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 2 test suites. 83: [----------] Global test environment set-up. 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -4.79910463671045e+01 83: Maximum force = 1.86297359432219e+02 on atom 13 83: Norm of force = 8.77219865482097e+01 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (283 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 3.02331e+02 on atom 3 83: F-Norm = 1.18024e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -5.58622538633256e+01 83: Maximum force = 4.27274822366624e+02 on atom 13 83: Norm of force = 1.84530029253875e+02 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (265 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.19376899751521e+02 83: Maximum force = 9.99884921009767e+03 on atom 9 83: Norm of force = 4.61669565054298e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (58 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: 83: NOTE 2 [file glycine_vacuo.top, line 12]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41575e+04 on atom 10 83: F-Norm = 1.18451e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.51743018140930e+02 83: Maximum force = 7.42089573409109e+03 on atom 9 83: Norm of force = 3.56929298615740e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (50 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.56984193848274e+02 83: Maximum force = 4.56923624626205e+02 on atom 17 83: Norm of force = 1.83258377168315e+02 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (8 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: 83: NOTE 3 [file unknown]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 1.06800e+03 on atom 28 83: F-Norm = 4.26922e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.69410778678182e+02 83: Maximum force = 2.18225948474131e+02 on atom 17 83: Norm of force = 7.92068036537818e+01 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (8 ms) 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (675 ms total) 83: 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents converged to Fmax < 10 in 1 steps 83: Potential Energy = -9.74257075835447e-01 83: Maximum force = 4.01322929015133e+00 on atom 1 83: Norm of force = 1.63839399694378e+00 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (3 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 83: Potential Energy = -9.90642313893957e-01 83: Maximum force = 2.57812909491104e+00 on atom 1 83: Norm of force = 1.05251679559258e+00 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (3 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 83: Potential Energy = -9.90642313893957e-01 83: Maximum force = 2.57812909491104e+00 on atom 1 83: Norm of force = 1.05251679559258e+00 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.19395484891520e+02 83: Maximum force = 9.97041707197911e+03 on atom 9 83: Norm of force = 4.62274878665467e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (50 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.56258793899481e+02 83: Maximum force = 7.50181017480396e+03 on atom 9 83: Norm of force = 3.61390332564874e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (49 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization has stopped, but the forces have not converged to the 83: requested precision Fmax < 10 (which may not be possible for your system). It 83: stopped because the algorithm tried to make a new step whose size was too 83: small, or there was no change in the energy since last step. Either way, we 83: regard the minimization as converged to within the available machine 83: precision, given your starting configuration and EM parameters. 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 83: but did not reach the requested Fmax < 10. 83: Potential Energy = 5.61116097794205e+02 83: Maximum force = 1.26854826291223e+04 on atom 10 83: Norm of force = 6.06436286976271e+03 83: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (49 ms) 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (161 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 2 test suites ran. (862 ms total) 83: [ PASSED ] 12 tests. 83/104 Test #83: Minimize1RankTests ........................ Passed 0.88 sec test 84 Start 84: Minimize2RankTests 84: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 12 tests from 2 test suites. 84: [----------] Global test environment set-up. 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -4.79910463671047e+01 84: Maximum force = 1.86297359432218e+02 on atom 13 84: Norm of force = 8.77219865482097e+01 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (287 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 3.02331e+02 on atom 3 84: F-Norm = 1.18024e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -5.58622538633258e+01 84: Maximum force = 4.27274822366617e+02 on atom 13 84: Norm of force = 1.84530029253872e+02 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (263 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.19376899751522e+02 84: Maximum force = 9.99884921009767e+03 on atom 9 84: Norm of force = 4.61669565054298e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (52 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: 84: NOTE 2 [file glycine_vacuo.top, line 12]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41575e+04 on atom 10 84: F-Norm = 1.18451e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.51743018140930e+02 84: Maximum force = 7.42089573409109e+03 on atom 9 84: Norm of force = 3.56929298615740e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (52 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.56984193848274e+02 84: Maximum force = 4.56923624626205e+02 on atom 17 84: Norm of force = 1.83258377168315e+02 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (10 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: 84: NOTE 3 [file unknown]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 1.06800e+03 on atom 28 84: F-Norm = 4.26922e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.69410778678182e+02 84: Maximum force = 2.18225948474131e+02 on atom 17 84: Norm of force = 7.92068036537818e+01 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (10 ms) 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (677 ms total) 84: 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents converged to Fmax < 10 in 1 steps 84: Potential Energy = -9.74257075835447e-01 84: Maximum force = 4.01322929015133e+00 on atom 3 84: Norm of force = 1.63839399694378e+00 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (4 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 4.01323e+00 on atom 3 84: F-Norm = 1.63839e+00 84: 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 84: Potential Energy = -9.90642313893957e-01 84: Maximum force = 2.57812909491104e+00 on atom 3 84: Norm of force = 1.05251679559258e+00 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (4 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.19395484891520e+02 84: Maximum force = 9.97041707197911e+03 on atom 9 84: Norm of force = 4.62274878665467e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (52 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41672e+04 on atom 10 84: F-Norm = 1.19357e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.56258793899481e+02 84: Maximum force = 7.50181017480396e+03 on atom 9 84: Norm of force = 3.61390332564874e+03 84: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (51 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (49 ms) 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (166 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 12 tests from 2 test suites ran. (871 ms total) 84: [ PASSED ] 12 tests. 84/104 Test #84: Minimize2RankTests ........................ Passed 0.89 sec test 85 Start 85: MdrunNonIntegratorTests 85: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 53 tests from 5 test suites. 85: [----------] Global test environment set-up. 85: [----------] 1 test from NonbondedBenchTest 85: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 85: SIMD width: 2 85: System size: 3000 atoms 85: Cut-off radius: 1 nm 85: Number of threads: 1 85: Number of iterations: 1 85: Compute energies: no 85: Ewald excl. corr.: analytical 85: 85: Coulomb LJ comb. SIMD intmod. Mcycles Mcycles/it. pairs/cycle 85: total useful 85: Ewald all geom. 4xM PotShift 25.626 25.6261 0.0413 0.0246 85: [ OK ] NonbondedBenchTest.BasicEndToEndTest (33 ms) 85: [----------] 1 test from NonbondedBenchTest (33 ms total) 85: 85: [----------] 5 tests from NormalModesWorks/NormalModesTest 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 15.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=6), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation '2 scaled waters' 85: 12 steps. 85: 85: Maximum force: 9.96989e-06 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.1-Debian_2026.1_1 85: 85: Diagonalizing to find vectors 7 through 18... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--18 to eigenvec.trr 85: Generated 3 of the 3 non-bonded parameter combinations 85: 85: Generated 3 of the 3 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: This run will generate roughly 0 Mb of data 85: There are: 6 Atoms 85: Using begin = 7 and end = 18 85: Full matrix storage format, nrow=18, ncols=18 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (6 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 1 85: 85: NOTE 2 [file villin.top, line 2452]: 85: System has non-zero total charge: -2.000000 85: Total charge should normally be an integer. See 85: https://manual.gromacs.org/current/user-guide/floating-point.html 85: for discussion on how close it should be to an integer. 85: 85: 85: 85: Number of degrees of freedom in T-Coupling group System is 765.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=256), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 85: 512 steps. 85: 85: Maximum force: 6.97568e-04 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.1-Debian_2026.1_1 85: 85: Diagonalizing to find vectors 7 through 50... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--50 to eigenvec.trr 85: Generated 20503 of the 20503 non-bonded parameter combinations 85: 85: Generated 17396 of the 20503 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 85: 85: This run will generate roughly 0 Mb of data 85: There are: 256 Atoms 85: Using begin = 7 and end = 50 85: Full matrix storage format, nrow=768, ncols=768 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (921 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 15.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=6), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation 'flex spc dimer' 85: 12 steps. 85: 85: Maximum force: 3.36401e-04 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.1-Debian_2026.1_1 85: 85: Diagonalizing to find vectors 7 through 18... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--18 to eigenvec.trr 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: This run will generate roughly 0 Mb of data 85: There are: 6 Atoms 85: Using begin = 7 and end = 18 85: Full matrix storage format, nrow=18, ncols=18 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (271 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 6.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=3), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation '1 TIP5P' 85: 6 steps. 85: 85: Maximum force: 2.42882e-04 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.1-Debian_2026.1_1 85: 85: Diagonalizing to find vectors 7 through 9... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--9 to eigenvec.trr 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: This run will generate roughly 0 Mb of data 85: There are: 3 Atoms 85: There are: 2 VSites 85: Using begin = 7 and end = 9 85: Full matrix storage format, nrow=9, ncols=9 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (273 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 85: Number of degrees of freedom in T-Coupling group System is 15.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There was 1 NOTE 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=6), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation 'sw dimer' 85: 12 steps. 85: 85: Maximum force: 1.07599e-03 85: The force is probably not small enough to ensure that you are at a minimum. 85: Be aware that negative eigenvalues may occur 85: when the resulting matrix is diagonalized. 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.1-Debian_2026.1_1 85: 85: Diagonalizing to find vectors 7 through 18... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--18 to eigenvec.trr 85: Generated 6 of the 10 non-bonded parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SW' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: This run will generate roughly 0 Mb of data 85: There are: 6 Atoms 85: There are: 2 Shells 85: There are: 2 VSites 85: 85: NOTE: in the current version shell prediction during the crun is disabled 85: 85: Using begin = 7 and end = 18 85: Full matrix storage format, nrow=18, ncols=18 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (6 ms) 85: [----------] 5 tests from NormalModesWorks/NormalModesTest (1479 ms total) 85: 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 139.229 0.172 0.621 0.019 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 85: 85: trr version: GMX_trn_file (double precision) 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 26 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4275.221 0.006 0.020 0.594 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (16 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 199.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 166.814 0.144 0.518 0.023 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 23 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 193.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3918.953 0.006 0.022 0.544 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (14 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 195.302 0.123 0.442 0.027 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 193.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2577.654 0.009 0.034 0.358 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (16 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 189.498 0.127 0.456 0.026 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 25 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 193.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3546.686 0.007 0.024 0.493 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (14 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 198.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 182.358 0.132 0.474 0.032 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 24 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3474.672 0.007 0.025 0.603 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (287 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.010 199.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 141.930 0.169 0.609 0.025 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 24 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 192.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3691.189 0.007 0.023 0.641 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (290 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.008 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 175.571 0.137 0.492 0.030 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 23 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 193.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3344.513 0.007 0.026 0.581 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (279 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 180.066 0.133 0.480 0.031 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 25 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 193.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3381.226 0.007 0.026 0.587 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (275 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 152.645 0.157 0.566 0.051 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 195.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2236.962 0.011 0.039 0.751 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (24 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 153.424 0.156 0.563 0.051 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 195.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2325.630 0.010 0.037 0.781 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (23 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 135.172 0.178 0.639 0.045 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 191.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1881.672 0.013 0.046 0.632 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (91 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 143.754 0.167 0.601 0.048 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 194.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2415.919 0.010 0.036 0.811 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (48 ms) 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1383 ms total) 85: 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 143.373 0.167 0.603 0.060 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1903.768 0.013 0.045 0.793 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 111.462 0.215 0.775 0.046 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1834.056 0.013 0.047 0.764 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (26 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 198.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 135.124 0.178 0.639 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1723.243 0.014 0.050 0.718 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 129.066 0.186 0.669 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1740.772 0.014 0.050 0.725 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (25 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.997 0.178 0.640 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1777.949 0.013 0.049 0.741 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.194 0.179 0.644 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1814.074 0.013 0.048 0.756 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 133.888 0.179 0.645 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1767.239 0.014 0.049 0.736 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 124.434 0.193 0.694 0.052 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1934.860 0.012 0.045 0.806 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 129.803 0.185 0.666 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 180.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1680.926 0.014 0.051 0.700 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 139.475 0.172 0.619 0.058 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1876.513 0.013 0.046 0.782 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 133.044 0.180 0.649 0.055 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1724.690 0.014 0.050 0.719 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 130.322 0.184 0.663 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 183.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1865.716 0.013 0.046 0.777 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.013 199.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 109.807 0.219 0.787 0.046 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 187.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1015.762 0.024 0.085 0.423 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (29 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 104.029 0.231 0.831 0.043 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 186.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1066.585 0.023 0.081 0.444 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (36 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 136.902 0.175 0.631 0.057 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1578.425 0.015 0.055 0.658 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (29 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 133.470 0.180 0.647 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1972.652 0.012 0.044 0.822 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 127.051 0.189 0.680 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1808.747 0.013 0.048 0.754 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 115.549 0.208 0.748 0.048 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 181.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1771.304 0.014 0.049 0.738 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (25 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 126.764 0.189 0.682 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1947.706 0.012 0.044 0.812 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 128.630 0.187 0.672 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1727.592 0.014 0.050 0.720 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 127.438 0.188 0.678 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1768.253 0.014 0.049 0.737 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 131.715 0.182 0.656 0.055 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 184.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1692.936 0.014 0.051 0.705 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 128.702 0.186 0.671 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 186.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1890.913 0.013 0.046 0.788 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (33 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 124.108 0.193 0.696 0.052 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 181.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1943.405 0.012 0.044 0.810 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (34 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 134.478 0.178 0.642 0.056 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1605.994 0.015 0.054 0.669 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (34 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 114.184 0.210 0.757 0.048 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1747.191 0.014 0.049 0.728 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (43 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 128.071 0.187 0.675 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1747.686 0.014 0.049 0.728 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (34 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 139.326 0.172 0.620 0.058 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1730.504 0.014 0.050 0.721 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 127.951 0.188 0.675 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 183.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1105.833 0.022 0.078 0.461 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (38 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 126.012 0.190 0.686 0.053 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 186.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1700.412 0.014 0.051 0.709 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (42 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 129.509 0.185 0.667 0.054 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1801.870 0.013 0.048 0.751 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (34 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.012 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 117.744 0.204 0.734 0.049 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 185.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1945.246 0.012 0.044 0.811 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (35 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 131.384 0.183 0.658 0.055 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 185.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1598.908 0.015 0.054 0.666 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (34 ms) 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (959 ms total) 85: 85: [----------] 2 tests from Angles1/SimpleMdrunTest 85: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 85: 85: NOTE 1 [file angles1.top, line 72]: 85: In moleculetype 'butane' 4 atoms are not bound by a potential or 85: constraint to any other atom in the same moleculetype. Although 85: technically this might not cause issues in a simulation, this often means 85: that the user forgot to add a bond/potential/constraint or put multiple 85: molecules in the same moleculetype definition by mistake. Run with -v to 85: get information for each atom. 85: 85: Number of degrees of freedom in T-Coupling group System is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 238.919 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'This_incredible_box_of_butane' 85: 50 steps, 0.1 ps. 85: Generated 3 of the 3 non-bonded parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'butane' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/angles1.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 444.370 0.054 0.194 0.021 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 85: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (14 ms) 85: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 85: 85: NOTE 1 [file angles1.top, line 72]: 85: In moleculetype 'butane' 4 atoms are not bound by a potential or 85: constraint to any other atom in the same moleculetype. Although 85: technically this might not cause issues in a simulation, this often means 85: that the user forgot to add a bond/potential/constraint or put multiple 85: molecules in the same moleculetype definition by mistake. Run with -v to 85: get information for each atom. 85: 85: Number of degrees of freedom in T-Coupling group System is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 238.919 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'This_incredible_box_of_butane' 85: 50 steps, 0.1 ps. 85: Generated 3 of the 3 non-bonded parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'butane' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/angles1.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.008 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 526.127 0.046 0.164 0.024 85: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 85: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (12 ms) 85: [----------] 2 tests from Angles1/SimpleMdrunTest (27 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 53 tests from 5 test suites ran. (3935 ms total) 85: [ PASSED ] 53 tests. 85/104 Test #85: MdrunNonIntegratorTests ................... Passed 3.95 sec test 86 Start 86: MdrunTpiTests 86: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 3 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 3 tests from Simple/TpiTest 86: [ RUN ] Simple/TpiTest.ReproducesOutput/0 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/0 (288 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/1 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/1 (272 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/2 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/2 (290 ms) 86: [----------] 3 tests from Simple/TpiTest (851 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 3 tests from 1 test suite ran. (865 ms total) 86: [ PASSED ] 3 tests. 86/104 Test #86: MdrunTpiTests ............................. Passed 0.88 sec test 87 Start 87: MdrunMpiTests 87: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 16 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from MimicTest 87: [ RUN ] MimicTest.OneQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 27 % of the run time was spent in domain decomposition, 87: 14 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 379.5 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 281.466 0.085 0.307 0.039 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -26222613 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.OneQuantumMol (6 ms) 87: [ RUN ] MimicTest.AllQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 31 % of the run time was spent in domain decomposition, 87: 15 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 381.3 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 284.896 0.084 0.303 0.040 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1170219081 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.AllQuantumMol (4 ms) 87: [ RUN ] MimicTest.TwoQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 27 % of the run time was spent in domain decomposition, 87: 13 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 381.1 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 284.672 0.084 0.304 0.040 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -137626130 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.TwoQuantumMol (4 ms) 87: [ RUN ] MimicTest.BondCuts 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 66.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: NVE simulation: will use the initial temperature of 300.368 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 87: 87: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 20 % of the run time was spent in domain decomposition, 87: 11 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.000 385.4 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 218.240 0.110 0.396 0.058 87: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -59787281 87: 87: Generated 2211 of the 2211 non-bonded parameter combinations 87: 87: Generated 2211 of the 2211 1-4 parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/ala.gro' 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.BondCuts (14 ms) 87: [----------] 4 tests from MimicTest (30 ms total) 87: 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: There was 1 NOTE 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There were 2 NOTEs 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There was 1 NOTE 87: Setting the LD random seed to 466476407 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to 1837104813 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -1091323361 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -21004326 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was turned on during the run due to measured imbalance. 87: Average load imbalance: 5.0%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.5%. 87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 87: 87: 87: NOTE: 40 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.026 0.006 397.5 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 279.908 0.086 0.309 0.019 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (9 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 44 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.006 398.5 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 300.636 0.080 0.287 0.021 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (8 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 8%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.043 0.011 397.2 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 167.155 0.144 0.517 0.012 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (148 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.053 0.013 397.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 136.405 0.176 0.633 0.009 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (85 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.047 0.012 398.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 153.304 0.157 0.564 0.011 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (26 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.047 0.012 397.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 154.034 0.156 0.561 0.011 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (23 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (303 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 16 tests from 2 test suites ran. (370 ms total) 87: [ PASSED ] 10 tests. 87: [ SKIPPED ] 6 tests, listed below: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87/104 Test #87: MdrunMpiTests ............................. Passed 0.38 sec test 88 Start 88: MdrunMultiSimTests 88: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 2 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from InNvt/MultiSimTerminationTest 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 88: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 2 tests from 1 test suite ran. (13 ms total) 88: [ PASSED ] 2 tests. 88: 88: YOU HAVE 4 DISABLED TESTS 88: 88/104 Test #88: MdrunMultiSimTests ........................ Passed 0.03 sec test 89 Start 89: MdrunMultiSimReplexTests 89: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 1 test from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 89: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 89: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 1 test from 1 test suite ran. (14 ms total) 89: [ PASSED ] 1 test. 89: 89: YOU HAVE 4 DISABLED TESTS 89: 89/104 Test #89: MdrunMultiSimReplexTests .................. Passed 0.03 sec test 90 Start 90: MdrunMultiSimReplexEquivalenceTests 90: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 0 tests from 0 test suites. 90: [==========] 0 tests from 0 test suites ran. (0 ms total) 90: [ PASSED ] 0 tests. 90: 90: YOU HAVE 10 DISABLED TESTS 90: 90/104 Test #90: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.01 sec test 91 Start 91: MdrunMpi1RankPmeTests 91: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 91: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 19 tests from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 19 tests from ReproducesEnergies/PmeTest 91: Number of degrees of freedom in T-Coupling group rest is 12.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 1046.791 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 2 NOTEs 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: For a correct single-point energy evaluation with nsteps = 0, use 91: continuation = yes to avoid constraining the input coordinates. 91: 91: Number of degrees of freedom in T-Coupling group rest is 13.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 966.268 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 3 NOTEs 91: Setting the LD random seed to 1932357437 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: Setting the LD random seed to -39593510 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: Searching the wall atom type(s) 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.031 0.016 199.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 116.193 0.207 0.744 0.008 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (156 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.030 0.015 199.5 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 119.289 0.201 0.724 0.008 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (20 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.004 0.002 194.5 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 42.755 0.561 2.021 0.003 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (479 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 91: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 91: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.034 0.017 199.6 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 107.265 0.224 0.805 0.007 91: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (22 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [----------] 19 tests from ReproducesEnergies/PmeTest (679 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 19 tests from 1 test suite ran. (699 ms total) 91: [ PASSED ] 4 tests. 91: [ SKIPPED ] 15 tests, listed below: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91/104 Test #91: MdrunMpi1RankPmeTests ..................... Passed 0.71 sec test 92 Start 92: MdrunMpi2RankPmeTests 92: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 19 tests from 1 test suite. 92: [----------] Global test environment set-up. 92: [----------] 19 tests from ReproducesEnergies/PmeTest 92: Number of degrees of freedom in T-Coupling group rest is 12.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 1046.791 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 2 NOTEs 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: For a correct single-point energy evaluation with nsteps = 0, use 92: continuation = yes to avoid constraining the input coordinates. 92: 92: Number of degrees of freedom in T-Coupling group rest is 13.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 966.268 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 3 NOTEs 92: Setting the LD random seed to -787489 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: Setting the LD random seed to -10880137 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: Searching the wall atom type(s) 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.2%. 92: The balanceable part of the MD step is 12%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.0%. 92: 92: 92: NOTE: 25 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.051 0.013 398.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 142.809 0.168 0.605 0.010 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (153 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.0%. 92: The balanceable part of the MD step is 11%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.9%. 92: 92: 92: NOTE: 26 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.048 0.012 398.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 150.983 0.159 0.572 0.010 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (19 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.005 0.001 378.1 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 61.157 0.392 1.413 0.004 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (446 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.053 0.013 398.1 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 136.451 0.176 0.633 0.009 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (86 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.048 0.012 397.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 150.747 0.159 0.573 0.010 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (17 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.007 0.002 386.0 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 44.698 0.537 1.933 0.003 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (332 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 92: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 9.1%. 92: The balanceable part of the MD step is 11%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.0%. 92: 92: 92: NOTE: 27 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.051 0.013 398.7 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 142.636 0.168 0.606 0.010 92: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (19 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [----------] 19 tests from ReproducesEnergies/PmeTest (1074 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 19 tests from 1 test suite ran. (1094 ms total) 92: [ PASSED ] 7 tests. 92: [ SKIPPED ] 12 tests, listed below: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92/104 Test #92: MdrunMpi2RankPmeTests ..................... Passed 1.11 sec test 93 Start 93: MdrunMpi4RankPmeTests 93: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "1" "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunMpi4RankPmeTests.xml" 93: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 93: Test timeout computed to be: 600 93: [==========] Running 19 tests from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 19 tests from ReproducesEnergies/PmeTest 93: Number of degrees of freedom in T-Coupling group rest is 12.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 1046.791 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 2 NOTEs 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: For a correct single-point energy evaluation with nsteps = 0, use 93: continuation = yes to avoid constraining the input coordinates. 93: 93: Number of degrees of freedom in T-Coupling group rest is 13.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 966.268 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 3 NOTEs 93: Setting the LD random seed to 1912322556 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: Setting the LD random seed to -581174817 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: Searching the wall atom type(s) 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 15.2%. 93: The balanceable part of the MD step is 8%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 1.2%. 93: 93: 93: NOTE: 43 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.050 0.013 398.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 145.149 0.165 0.595 0.010 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (150 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 9.9%. 93: The balanceable part of the MD step is 8%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.7%. 93: 93: 93: NOTE: 40 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.040 0.010 398.2 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 180.255 0.133 0.479 0.013 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (16 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.006 0.001 375.7 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 57.933 0.414 1.491 0.004 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (443 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 24.1%. 93: The balanceable part of the MD step is 3%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.7%. 93: Average PME mesh/force load: 52.927 93: Part of the total run time spent waiting due to PP/PME imbalance: 71.1 % 93: 93: NOTE: 71.1 % performance was lost because the PME ranks 93: had more work to do than the PP ranks. 93: You might want to increase the number of PME ranks 93: or increase the cut-off and the grid spacing. 93: 93: 93: NOTE: 23 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.089 0.022 399.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 81.753 0.294 1.057 0.006 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (82 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 21.4%. 93: The balanceable part of the MD step is 4%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.9%. 93: Average PME mesh/force load: 36.216 93: Part of the total run time spent waiting due to PP/PME imbalance: 69.4 % 93: 93: NOTE: 69.4 % performance was lost because the PME ranks 93: had more work to do than the PP ranks. 93: You might want to increase the number of PME ranks 93: or increase the cut-off and the grid spacing. 93: 93: 93: NOTE: 16 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.081 0.020 399.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 89.797 0.267 0.962 0.006 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (23 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.012 0.003 375.6 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 27.995 0.857 3.086 0.002 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (134 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 93: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 93: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 11.7%. 93: The balanceable part of the MD step is 7%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.9%. 93: 93: 93: NOTE: 42 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.041 0.010 397.3 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 173.967 0.138 0.497 0.012 93: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (17 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [----------] 19 tests from ReproducesEnergies/PmeTest (869 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 19 tests from 1 test suite ran. (888 ms total) 93: [ PASSED ] 7 tests. 93: [ SKIPPED ] 12 tests, listed below: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93/104 Test #93: MdrunMpi4RankPmeTests ..................... Passed 0.90 sec test 94 Start 94: MdrunCoordinationBasicTests1Rank 94: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 94: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 94: Test timeout computed to be: 1920 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest 94: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.009 0.009 99.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 156.396 0.153 0.552 0.022 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.005 0.005 99.5 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 295.345 0.081 0.293 0.041 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 4. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 4. 94: 94: 94: There were 4 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.005 0.005 99.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 268.202 0.089 0.322 0.037 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.008 0.008 99.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 193.711 0.124 0.446 0.027 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.008 0.008 99.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 188.179 0.128 0.459 0.026 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 94: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.007 0.007 99.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 208.565 0.115 0.414 0.029 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (64 ms) 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest (64 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (78 ms total) 94: [ PASSED ] 1 test. 94/104 Test #94: MdrunCoordinationBasicTests1Rank .......... Passed 0.09 sec test 95 Start 95: MdrunCoordinationBasicTests2Ranks 95: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 95: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 95: Test timeout computed to be: 1920 95: [==========] Running 1 test from 1 test suite. 95: [----------] Global test environment set-up. 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest 95: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 0.6%. 95: The balanceable part of the MD step is 57%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.3%. 95: 95: 95: NOTE: 47 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.022 0.011 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 130.800 0.183 0.661 0.018 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.6%. 95: The balanceable part of the MD step is 55%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.9%. 95: 95: 95: NOTE: 46 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.008 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 183.479 0.131 0.471 0.025 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 4 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.8%. 95: The balanceable part of the MD step is 50%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.9%. 95: 95: 95: NOTE: 46 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.006 198.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 264.858 0.091 0.326 0.037 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.9%. 95: The balanceable part of the MD step is 50%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 1.0%. 95: 95: 95: NOTE: 47 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.008 198.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 188.348 0.127 0.459 0.026 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.6%. 95: The balanceable part of the MD step is 50%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.8%. 95: 95: 95: NOTE: 47 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.007 199.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 200.000 0.120 0.432 0.028 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 95: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.6%. 95: The balanceable part of the MD step is 47%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.7%. 95: 95: 95: NOTE: 47 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.017 0.009 199.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 168.825 0.142 0.512 0.023 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (75 ms) 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest (75 ms total) 95: 95: [----------] Global test environment tear-down 95: [==========] 1 test from 1 test suite ran. (89 ms total) 95: [ PASSED ] 1 test. 95/104 Test #95: MdrunCoordinationBasicTests2Ranks ......... Passed 0.10 sec test 96 Start 96: MdrunCoordinationCouplingTests1Rank 96: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 96: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 96: Test timeout computed to be: 1920 96: [==========] Running 25 tests from 1 test suite. 96: [----------] Global test environment set-up. 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 158.013 0.152 0.547 0.022 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 236.119 0.102 0.366 0.033 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 281.421 0.085 0.307 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 203.112 0.118 0.425 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 201.136 0.119 0.430 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 177.488 0.135 0.487 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (66 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 152.452 0.157 0.567 0.021 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 266.254 0.090 0.325 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 246.858 0.097 0.350 0.034 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 196.035 0.122 0.441 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 208.742 0.115 0.414 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.842 0.127 0.458 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 171.270 0.140 0.504 0.024 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 257.981 0.093 0.335 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 275.926 0.087 0.313 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 166.072 0.145 0.520 0.023 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 205.703 0.117 0.420 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 212.281 0.113 0.407 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (66 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 199.411 0.120 0.433 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 270.653 0.089 0.319 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 281.537 0.085 0.307 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.118 0.112 0.404 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 216.101 0.111 0.400 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.269 0.125 0.452 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (62 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 185.476 0.129 0.466 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 211.653 0.113 0.408 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 296.982 0.081 0.291 0.041 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.723 0.124 0.446 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 196.304 0.122 0.440 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 196.567 0.122 0.440 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 167.914 0.143 0.515 0.023 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 249.144 0.096 0.347 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 296.667 0.081 0.291 0.041 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 182.954 0.131 0.472 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 206.523 0.116 0.418 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 206.136 0.116 0.419 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.153 0.123 0.443 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 271.344 0.088 0.318 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 233.710 0.103 0.370 0.032 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.392 0.117 0.423 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 151.021 0.159 0.572 0.021 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 169.639 0.141 0.509 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (67 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.608 0.125 0.451 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 283.324 0.085 0.305 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 267.190 0.090 0.323 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.415 0.127 0.459 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.019 0.124 0.448 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 201.465 0.119 0.429 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (61 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.376 0.123 0.442 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 272.677 0.088 0.317 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 225.374 0.106 0.383 0.031 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 210.116 0.114 0.411 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.225 0.124 0.447 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.513 0.112 0.403 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (63 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 200.815 0.120 0.430 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 251.504 0.095 0.344 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 292.776 0.082 0.295 0.041 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.973 0.122 0.441 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.264 0.134 0.482 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 207.861 0.115 0.416 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 187.150 0.128 0.462 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 259.930 0.092 0.332 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 274.133 0.088 0.315 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.048 0.123 0.443 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 202.179 0.119 0.427 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 157.074 0.153 0.550 0.022 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (66 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.660 0.126 0.453 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 261.164 0.092 0.331 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 303.942 0.079 0.284 0.042 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.104 0.124 0.447 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 185.460 0.129 0.466 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 180.880 0.133 0.478 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 202.219 0.119 0.427 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 250.390 0.096 0.345 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 283.324 0.085 0.305 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 200.019 0.120 0.432 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 215.375 0.111 0.401 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 194.820 0.123 0.443 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (62 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 194.010 0.124 0.445 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 277.917 0.086 0.311 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 269.257 0.089 0.321 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 192.050 0.125 0.450 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 207.392 0.116 0.417 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.912 0.127 0.457 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (63 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 210.331 0.114 0.411 0.029 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 271.655 0.088 0.318 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 275.901 0.087 0.313 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 212.478 0.113 0.407 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 205.428 0.117 0.421 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 228.627 0.105 0.378 0.032 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (59 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 200.599 0.120 0.431 0.028 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 168.663 0.142 0.512 0.023 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 313.788 0.076 0.275 0.044 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.543 0.112 0.403 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 212.522 0.113 0.407 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 208.509 0.115 0.414 0.029 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (63 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 181.911 0.132 0.475 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 266.047 0.090 0.325 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 262.555 0.091 0.329 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.559 0.124 0.446 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 199.838 0.120 0.432 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 176.223 0.136 0.490 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (63 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 177.892 0.135 0.486 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 254.181 0.094 0.340 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 285.120 0.084 0.303 0.040 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.866 0.133 0.480 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.311 0.125 0.452 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 189.580 0.127 0.456 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 183.307 0.131 0.471 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 262.309 0.091 0.329 0.036 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 245.442 0.098 0.352 0.034 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.772 0.126 0.453 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 199.449 0.120 0.433 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 180.140 0.133 0.480 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (63 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.531 0.134 0.481 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 270.284 0.089 0.320 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 270.926 0.089 0.319 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.103 0.112 0.404 0.030 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 190.878 0.126 0.453 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 173.719 0.138 0.497 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (63 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 192.374 0.125 0.449 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 276.173 0.087 0.313 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 271.799 0.088 0.318 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.649 0.123 0.442 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 189.937 0.126 0.455 0.026 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 192.458 0.125 0.449 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (64 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 193.055 0.124 0.448 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 277.917 0.086 0.311 0.039 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 274.941 0.087 0.314 0.038 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 148.731 0.161 0.581 0.021 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 198.992 0.121 0.434 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 178.320 0.135 0.485 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (65 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 182.245 0.132 0.474 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 249.366 0.096 0.346 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 164.647 0.146 0.525 0.023 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.009 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 172.624 0.139 0.501 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 175.480 0.137 0.492 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 174.992 0.137 0.494 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (71 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 165.857 0.145 0.521 0.023 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.234 0.123 0.443 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 219.653 0.109 0.393 0.031 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 183.444 0.131 0.471 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 147.017 0.163 0.588 0.020 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.009 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 172.711 0.139 0.500 0.024 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (72 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.424 0.125 0.451 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 251.607 0.095 0.343 0.035 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 267.829 0.090 0.323 0.037 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 192.645 0.125 0.448 0.027 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 182.218 0.132 0.474 0.025 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 96: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 203.327 0.118 0.425 0.028 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (64 ms) 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (1621 ms total) 96: 96: [----------] Global test environment tear-down 96: [==========] 25 tests from 1 test suite ran. (1635 ms total) 96: [ PASSED ] 25 tests. 96/104 Test #96: MdrunCoordinationCouplingTests1Rank ....... Passed 1.65 sec test 97 Start 97: MdrunCoordinationCouplingTests2Ranks 97: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 97: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 97: Test timeout computed to be: 1920 97: [==========] Running 25 tests from 1 test suite. 97: [----------] Global test environment set-up. 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.9%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.5%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 144.645 0.166 0.597 0.020 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.5%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.3%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 244.255 0.098 0.354 0.034 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.6%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 291.260 0.082 0.297 0.040 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 41%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 193.228 0.124 0.447 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 42%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 206.988 0.116 0.417 0.029 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.7%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 201.725 0.119 0.428 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (69 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.2%. 97: The balanceable part of the MD step is 54%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.1%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.394 0.128 0.461 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.8%. 97: The balanceable part of the MD step is 52%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.4%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 195.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 227.673 0.105 0.379 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 237.033 0.101 0.365 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.1%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 176.562 0.136 0.489 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 47%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.911 0.130 0.467 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.3%. 97: The balanceable part of the MD step is 47%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 197.398 0.122 0.438 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (72 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.8%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.132 0.130 0.469 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 50%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 236.047 0.102 0.366 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 266.433 0.090 0.324 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.4%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 197.797 0.121 0.437 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 35.9%. 97: The balanceable part of the MD step is 23%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 8.3%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 8.3 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 41 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 135.119 0.178 0.639 0.019 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 47%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.785 0.133 0.478 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (73 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.5%. 97: The balanceable part of the MD step is 53%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.3%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.920 0.130 0.467 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.8%. 97: The balanceable part of the MD step is 50%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.4%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 269.086 0.089 0.321 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.3%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 250.217 0.096 0.345 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.2%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 176.640 0.136 0.489 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 44%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 166.976 0.144 0.517 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 47%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.201 0.139 0.499 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (71 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 44 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 170.034 0.141 0.508 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 197.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 284.383 0.084 0.304 0.039 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 236.478 0.101 0.365 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 206.503 0.116 0.418 0.029 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.494 0.128 0.461 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 189.668 0.127 0.456 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (69 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.640 0.128 0.460 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 245.149 0.098 0.352 0.034 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.009 0.005 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 306.955 0.078 0.281 0.043 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 203.283 0.118 0.425 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 189.030 0.127 0.457 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.600 0.128 0.461 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (67 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 191.151 0.126 0.452 0.027 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.655 0.152 0.548 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 274.194 0.088 0.315 0.038 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.036 0.126 0.455 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 159.806 0.150 0.541 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 183.539 0.131 0.471 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (73 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.702 0.133 0.478 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 271.769 0.088 0.318 0.038 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 265.348 0.090 0.326 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 174.583 0.137 0.495 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.493 0.142 0.513 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 172.551 0.139 0.501 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (70 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 182.997 0.131 0.472 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 267.410 0.090 0.323 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 233.303 0.103 0.370 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 175.939 0.136 0.491 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.024 0.012 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 123.912 0.194 0.697 0.017 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.036 0.153 0.550 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (82 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 171.028 0.140 0.505 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 254.239 0.094 0.340 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 228.874 0.105 0.378 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.950 0.130 0.467 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 162.630 0.148 0.531 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 160.226 0.150 0.539 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (84 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.529 0.128 0.461 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 230.600 0.104 0.375 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 215.518 0.111 0.401 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 191.677 0.125 0.451 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 186.733 0.129 0.463 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.495 0.126 0.454 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (72 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 186.821 0.128 0.462 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 262.142 0.092 0.330 0.036 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 235.398 0.102 0.367 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 183.611 0.131 0.471 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 188.297 0.127 0.459 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.712 0.142 0.512 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (70 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.228 0.139 0.499 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 232.195 0.103 0.372 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 264.483 0.091 0.327 0.037 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 186.247 0.129 0.464 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 192.968 0.124 0.448 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 178.646 0.134 0.484 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (77 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 177.718 0.135 0.486 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 256.232 0.094 0.337 0.036 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 237.654 0.101 0.364 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 189.045 0.127 0.457 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.633 0.133 0.478 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 197.746 0.121 0.437 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (75 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 186.461 0.129 0.463 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 251.669 0.095 0.343 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 253.137 0.095 0.341 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 189.496 0.127 0.456 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.575 0.133 0.478 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 200.172 0.120 0.432 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (75 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 166.123 0.144 0.520 0.023 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 262.209 0.092 0.330 0.036 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 250.268 0.096 0.345 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 201.987 0.119 0.428 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 198.626 0.121 0.435 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 188.715 0.127 0.458 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (73 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 59%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 182.271 0.132 0.474 0.025 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 6.0%. 97: The balanceable part of the MD step is 61%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 3.7%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 230.354 0.104 0.375 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 4.3%. 97: The balanceable part of the MD step is 50%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 2.1%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 224.119 0.107 0.386 0.031 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 6.4%. 97: The balanceable part of the MD step is 50%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 3.2%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 188.481 0.127 0.458 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 4.8%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 2.3%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.586 0.133 0.478 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.3%. 97: The balanceable part of the MD step is 53%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.513 0.138 0.498 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (74 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.6%. 97: The balanceable part of the MD step is 61%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.3%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.837 0.138 0.497 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 3.7%. 97: The balanceable part of the MD step is 55%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 2.0%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 196.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 207.302 0.116 0.417 0.029 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.0%. 97: The balanceable part of the MD step is 55%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 237.865 0.101 0.363 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.2%. 97: The balanceable part of the MD step is 57%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 183.526 0.131 0.471 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 4.1%. 97: The balanceable part of the MD step is 55%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 2.2%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.766 0.133 0.478 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.8%. 97: The balanceable part of the MD step is 56%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 179.919 0.133 0.480 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (76 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.2%. 97: The balanceable part of the MD step is 57%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.850 0.142 0.512 0.023 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 59%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 252.354 0.095 0.342 0.035 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.7%. 97: The balanceable part of the MD step is 58%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 240.498 0.100 0.359 0.033 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 53%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 169.753 0.141 0.509 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 7.0%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 3.6%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 197.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 150.751 0.159 0.573 0.021 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 56%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 159.779 0.150 0.541 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (78 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 197.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 154.835 0.155 0.558 0.022 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 214.670 0.112 0.402 0.030 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 196.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 222.585 0.108 0.388 0.031 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 166.638 0.144 0.518 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 156.000 0.154 0.554 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 142.249 0.169 0.607 0.020 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (82 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.721 0.138 0.497 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 200.413 0.120 0.431 0.028 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 231.063 0.104 0.374 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.520 0.142 0.513 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 166.471 0.144 0.519 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.026 0.013 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 112.590 0.213 0.767 0.016 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (79 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 159.972 0.150 0.540 0.022 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 227.446 0.106 0.380 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 246.335 0.097 0.351 0.034 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 169.992 0.141 0.508 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 154.939 0.155 0.558 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 182.571 0.131 0.473 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (74 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 158.248 0.152 0.546 0.022 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.860 0.126 0.453 0.027 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 162.283 0.148 0.532 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 149.456 0.161 0.578 0.021 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.285 0.133 0.479 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 196.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.054 0.153 0.550 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (79 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.010 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 140.614 0.171 0.614 0.020 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 196.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 178.521 0.134 0.484 0.025 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 188.894 0.127 0.457 0.026 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 155.561 0.154 0.555 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.887 0.142 0.512 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.120 0.153 0.550 0.022 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (88 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.457 0.138 0.498 0.024 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 232.717 0.103 0.371 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.006 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 228.056 0.105 0.379 0.032 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 168.837 0.142 0.512 0.023 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 169.259 0.142 0.510 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 97: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 172.907 0.139 0.500 0.024 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (73 ms) 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (1887 ms total) 97: 97: [----------] Global test environment tear-down 97: [==========] 25 tests from 1 test suite ran. (1902 ms total) 97: [ PASSED ] 25 tests. 97/104 Test #97: MdrunCoordinationCouplingTests2Ranks ...... Passed 1.91 sec test 98 Start 98: MdrunCoordinationConstraintsTests1Rank 98: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 98: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 98: Test timeout computed to be: 1920 98: [==========] Running 13 tests from 1 test suite. 98: [----------] Global test environment set-up. 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 127.596 0.188 0.677 0.022 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 202.925 0.118 0.426 0.035 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 224.700 0.107 0.385 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 186.792 0.128 0.463 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 189.820 0.126 0.455 0.033 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 162.317 0.148 0.532 0.028 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1720 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 132.304 0.181 0.653 0.023 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 219.176 0.110 0.394 0.038 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 203.501 0.118 0.425 0.035 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 184.328 0.130 0.469 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 168.203 0.143 0.514 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 166.480 0.144 0.519 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1604 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 176.775 0.136 0.489 0.031 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 235.497 0.102 0.367 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 247.354 0.097 0.349 0.043 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 183.876 0.131 0.470 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 200.221 0.120 0.432 0.035 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 189.808 0.126 0.455 0.033 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1737 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 131.303 0.183 0.658 0.023 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 226.019 0.106 0.382 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 218.631 0.110 0.395 0.038 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 186.634 0.129 0.463 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 203.764 0.118 0.424 0.035 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 191.955 0.125 0.450 0.033 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1684 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 156.742 0.153 0.551 0.027 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 237.531 0.101 0.364 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 244.662 0.098 0.353 0.042 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 182.078 0.132 0.475 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 168.709 0.142 0.512 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 156.103 0.154 0.553 0.027 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1636 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 162.330 0.148 0.532 0.028 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 252.545 0.095 0.342 0.044 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 98.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 243.338 0.099 0.355 0.042 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 169.713 0.141 0.509 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 152.603 0.157 0.566 0.026 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 156.706 0.153 0.551 0.027 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1696 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 173.910 0.138 0.497 0.030 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.010 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 153.980 0.156 0.561 0.027 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 240.667 0.100 0.359 0.042 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 181.557 0.132 0.476 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 173.895 0.138 0.497 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 180.066 0.133 0.480 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1682 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 166.287 0.144 0.520 0.029 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 229.419 0.105 0.377 0.040 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 212.926 0.113 0.406 0.037 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 171.270 0.140 0.504 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 148.534 0.162 0.582 0.026 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 172.295 0.139 0.501 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1653 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 174.338 0.138 0.496 0.030 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 241.204 0.100 0.358 0.042 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 232.388 0.103 0.372 0.040 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 174.997 0.137 0.494 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 177.324 0.135 0.487 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 155.417 0.154 0.556 0.027 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1678 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 164.480 0.146 0.525 0.029 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 235.443 0.102 0.367 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 226.060 0.106 0.382 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 185.225 0.130 0.466 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 180.024 0.133 0.480 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 176.805 0.136 0.489 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1659 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 172.842 0.139 0.500 0.030 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 228.551 0.105 0.378 0.040 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 213.761 0.112 0.404 0.037 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 173.484 0.138 0.498 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.011 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 139.633 0.172 0.619 0.024 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.011 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 139.459 0.172 0.620 0.024 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1667 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 162.996 0.147 0.530 0.028 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 222.292 0.108 0.389 0.039 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 218.236 0.110 0.396 0.038 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 111.836 0.215 0.773 0.019 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 181.691 0.132 0.476 0.032 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 172.914 0.139 0.500 0.030 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1659 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 174.744 0.137 0.494 0.030 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 209.195 0.115 0.413 0.036 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 234.636 0.102 0.368 0.041 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 157.681 0.152 0.548 0.027 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 178.377 0.135 0.484 0.031 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 98: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 167.108 0.144 0.517 0.029 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1649 ms) 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (21730 ms total) 98: 98: [----------] Global test environment tear-down 98: [==========] 13 tests from 1 test suite ran. (21745 ms total) 98: [ PASSED ] 13 tests. 98/104 Test #98: MdrunCoordinationConstraintsTests1Rank .... Passed 21.76 sec test 99 Start 99: MdrunCoordinationConstraintsTests2Ranks 99: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 99: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 99: Test timeout computed to be: 1920 99: [==========] Running 13 tests from 1 test suite. 99: [----------] Global test environment set-up. 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.7%. 99: The balanceable part of the MD step is 54%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 159.186 0.151 0.543 0.028 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 4.1%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 2.0%. 99: 99: 99: NOTE: 45 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 241.313 0.099 0.358 0.042 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.4%. 99: The balanceable part of the MD step is 44%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 205.521 0.117 0.420 0.036 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 3.0%. 99: The balanceable part of the MD step is 43%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.3%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 157.489 0.152 0.549 0.027 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.0%. 99: The balanceable part of the MD step is 47%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 164.649 0.146 0.525 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 4.4%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.7%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 181.876 0.132 0.475 0.032 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1688 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.8%. 99: The balanceable part of the MD step is 51%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.9%. 99: 99: 99: NOTE: 45 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 169.536 0.142 0.510 0.029 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.8%. 99: The balanceable part of the MD step is 47%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.3%. 99: 99: 99: NOTE: 43 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 213.332 0.113 0.405 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.7%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 212.823 0.113 0.406 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.2%. 99: The balanceable part of the MD step is 44%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 147.573 0.163 0.585 0.026 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.1%. 99: The balanceable part of the MD step is 45%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 166.764 0.144 0.518 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.6%. 99: The balanceable part of the MD step is 44%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.2%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.021 0.011 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 136.958 0.175 0.631 0.024 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1676 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.8%. 99: The balanceable part of the MD step is 53%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.021 0.010 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 141.848 0.169 0.609 0.025 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.0%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 45 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 204.389 0.117 0.423 0.035 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.8%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: NOTE: 45 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 233.056 0.103 0.371 0.040 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.0%. 99: The balanceable part of the MD step is 44%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 164.978 0.145 0.524 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.2%. 99: The balanceable part of the MD step is 45%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 173.795 0.138 0.497 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.1%. 99: The balanceable part of the MD step is 42%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.9%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 172.493 0.139 0.501 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1689 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 148.325 0.162 0.583 0.026 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 252.359 0.095 0.342 0.044 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 230.285 0.104 0.375 0.040 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 162.082 0.148 0.533 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 169.138 0.142 0.511 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 170.886 0.140 0.506 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1682 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 166.814 0.144 0.518 0.029 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 219.437 0.109 0.394 0.038 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 218.655 0.110 0.395 0.038 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 174.811 0.137 0.494 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.021 0.011 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 137.173 0.175 0.630 0.024 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 177.687 0.135 0.486 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1765 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.024 0.012 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 119.573 0.201 0.723 0.021 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 227.782 0.105 0.379 0.040 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 210.392 0.114 0.411 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 166.512 0.144 0.519 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 174.013 0.138 0.497 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 169.394 0.142 0.510 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1690 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 156.065 0.154 0.554 0.027 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 215.466 0.111 0.401 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 228.619 0.105 0.378 0.040 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 183.879 0.131 0.470 0.032 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 185.262 0.130 0.466 0.032 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 176.072 0.136 0.491 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1660 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 173.109 0.139 0.499 0.030 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 208.357 0.115 0.415 0.036 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 250.055 0.096 0.346 0.043 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 178.052 0.135 0.485 0.031 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 164.127 0.146 0.526 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 166.016 0.145 0.520 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1644 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 161.989 0.148 0.533 0.028 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 202.561 0.118 0.427 0.035 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 192.275 0.125 0.449 0.033 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 162.523 0.148 0.532 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 197.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 167.674 0.143 0.515 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 171.681 0.140 0.503 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1714 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.6%. 99: The balanceable part of the MD step is 60%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 147.921 0.162 0.584 0.026 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 57%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 198.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 185.331 0.129 0.466 0.032 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.4%. 99: The balanceable part of the MD step is 52%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.3%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 196.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 206.309 0.116 0.419 0.036 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.1%. 99: The balanceable part of the MD step is 49%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.0%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 197.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 171.368 0.140 0.504 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.5%. 99: The balanceable part of the MD step is 51%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 152.666 0.157 0.566 0.027 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.7%. 99: The balanceable part of the MD step is 51%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.9%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 166.868 0.144 0.518 0.029 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1705 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.6%. 99: The balanceable part of the MD step is 62%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.030 0.015 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 98.061 0.245 0.881 0.017 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.2%. 99: The balanceable part of the MD step is 59%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 213.015 0.113 0.406 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.4%. 99: The balanceable part of the MD step is 57%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 197.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 223.729 0.107 0.386 0.039 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.4%. 99: The balanceable part of the MD step is 54%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 158.936 0.151 0.544 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 51%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 160.981 0.149 0.537 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 55%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 151.726 0.158 0.569 0.026 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1680 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.022 0.011 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 130.224 0.184 0.663 0.023 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 197.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 204.260 0.117 0.423 0.035 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 212.772 0.113 0.406 0.037 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 197.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 162.320 0.148 0.532 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.023 0.012 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 124.298 0.193 0.695 0.022 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.008 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 174.655 0.137 0.495 0.030 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1664 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 198.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 111.631 0.215 0.774 0.019 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 197.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 186.741 0.129 0.463 0.032 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 196.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 223.145 0.108 0.387 0.039 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 163.195 0.147 0.529 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 159.566 0.150 0.541 0.028 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 99: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.028 0.014 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 105.121 0.228 0.822 0.018 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1719 ms) 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (21981 ms total) 99: 99: [----------] Global test environment tear-down 99: [==========] 13 tests from 1 test suite ran. (21997 ms total) 99: [ PASSED ] 13 tests. 99/104 Test #99: MdrunCoordinationConstraintsTests2Ranks ... Passed 22.02 sec test 100 Start 100: MdrunFEPTests 100: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 100: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 100: Test timeout computed to be: 600 100: [==========] Running 14 tests from 2 test suites. 100: [----------] Global test environment set-up. 100: [----------] 2 tests from ExpandedEnsembleTest 100: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 16 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.030 0.015 199.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 97.832 0.245 0.883 0.041 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 100: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 100: 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.025 0.012 199.1 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 62.732 0.383 1.377 0.026 100: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (58 ms) 100: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 1 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.022 0.011 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 15.692 1.529 5.506 0.007 100: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (25 ms) 100: [----------] 2 tests from ExpandedEnsembleTest (84 ms total) 100: 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -201852019 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.92 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.086 0.043 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 42.296 0.567 2.043 0.087 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 100: 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (272 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -328340161 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.92 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.101 0.050 199.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 36.001 0.667 2.400 0.074 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (137 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 2092826591 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.92 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.055 0.028 199.4 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 65.613 0.366 1.317 0.134 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (112 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 155]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 155]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to -4804615 100: 100: Generated 171 of the 171 non-bonded parameter combinations 100: 100: Generated 171 of the 171 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 358.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 1 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.95 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.063 0.032 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 57.057 0.421 1.514 0.118 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (214 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 165]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 165]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to -1093107842 100: 100: Generated 190 of the 190 non-bonded parameter combinations 100: 100: Generated 190 of the 190 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'CL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'CL' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 361.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 2 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.95 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.063 0.032 199.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 57.410 0.418 1.505 0.119 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (48 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 100: and vdw_modifier=Force-switch 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 100 steps, 0.1 ps. 100: Setting the LD random seed to -2244615 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.92 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.327 0.164 199.9 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 53.342 0.450 1.620 0.109 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (248 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There were 11 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 2063267571 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.92 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.144 0.072 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 25.164 0.954 3.433 0.052 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (155 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: Removing center of mass motion in the presence of position restraints 100: might cause artifacts. When you are using position restraints to 100: equilibrate a macro-molecule, the artifacts are usually negligible. 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There were 11 WARNINGs 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -1208090884 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.92 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.165 0.082 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 22.000 1.091 3.927 0.045 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (190 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -297816225 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.86 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.046 0.023 199.4 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 78.232 0.307 1.104 0.160 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (110 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: There was 1 NOTE 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.028 0.014 198.9 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 127.758 0.188 0.676 0.262 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: Setting the LD random seed to -137629764 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.86 100: 100: This run will generate roughly 0 Mb of data 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (94 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 1895299054 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.92 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.099 0.050 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 36.499 0.658 2.367 0.075 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (132 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 100: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -806913 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.86 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.049 0.025 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 73.468 0.327 1.176 0.151 100: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (108 ms) 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (1831 ms total) 100: 100: [----------] Global test environment tear-down 100: [==========] 14 tests from 2 test suites ran. (1942 ms total) 100: [ PASSED ] 14 tests. 100/104 Test #100: MdrunFEPTests ............................. Passed 1.96 sec test 101 Start 101: MdrunPullTests 101: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 101: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 101: Test timeout computed to be: 600 101: [==========] Running 4 tests from 1 test suite. 101: [----------] Global test environment set-up. 101: [----------] 4 tests from PullTest/PullIntegrationTest 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.600 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.046 0.023 199.6 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 77.961 0.308 1.108 0.585 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (298 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.301 nm 0.400 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.048 0.024 199.7 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 75.996 0.316 1.137 0.570 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (280 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Pull group 3 'r_3' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1292.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.357 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.500 nm 101: 1 3 2 101: 3 3 8 0.331 nm 0.400 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.043 0.022 199.6 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 83.708 0.287 1.032 0.628 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (277 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.000 nm 101: 0.050 nm 0.000 nm 101: 101: There was 1 NOTE 101: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 101: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.044 0.022 199.5 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 82.333 0.291 1.049 0.617 101: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (279 ms) 101: [----------] 4 tests from PullTest/PullIntegrationTest (1136 ms total) 101: 101: [----------] Global test environment tear-down 101: [==========] 4 tests from 1 test suite ran. (1151 ms total) 101: [ PASSED ] 4 tests. 101/104 Test #101: MdrunPullTests ............................ Passed 1.17 sec test 102 Start 102: MdrunRotationTests 102: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 102: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 102: Test timeout computed to be: 600 102: [==========] Running 12 tests from 1 test suite. 102: [----------] Global test environment set-up. 102: [----------] 12 tests from RotationWorks/RotationTest 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 102: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: trr version: GMX_trn_file (single precision) 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 924794875 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 374.598 0.064 0.461 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (18 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 102: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 2138699731 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.027 0.014 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 326.125 0.074 0.530 0.008 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (19 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 102: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -134217754 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.021 0.011 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 418.462 0.057 0.413 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (16 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 102: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1109945926 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.010 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 465.380 0.052 0.371 0.011 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (15 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 102: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -185222657 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.021 0.011 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 425.895 0.056 0.406 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (16 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 102: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 1740099582 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.023 0.012 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 383.807 0.063 0.450 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (17 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 102: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -404064777 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.010 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 469.988 0.051 0.368 0.011 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (15 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 102: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1077936153 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.020 0.010 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 455.624 0.053 0.379 0.011 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (15 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 102: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -306192425 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.021 0.011 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 425.713 0.056 0.406 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (16 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 102: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -84693317 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.023 0.011 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 390.974 0.061 0.442 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (16 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 102: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -336347257 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.021 0.010 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 433.399 0.055 0.399 0.010 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (16 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 102: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 102: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -135301157 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 374.889 0.064 0.461 0.009 102: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (19 ms) 102: [----------] 12 tests from RotationWorks/RotationTest (203 ms total) 102: 102: [----------] Global test environment tear-down 102: [==========] 12 tests from 1 test suite ran. (216 ms total) 102: [ PASSED ] 12 tests. 102/104 Test #102: MdrunRotationTests ........................ Passed 0.23 sec test 103 Start 103: MdrunSimulatorComparison 103: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 103: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 103: Test timeout computed to be: 600 103: [==========] Running 94 tests from 4 test suites. 103: [----------] Global test environment set-up. 103: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 145.948 0.164 0.592 0.020 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 181.975 0.132 0.475 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 103: 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (25 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 160.914 0.149 0.537 0.022 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 185.159 0.130 0.467 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (23 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 177.585 0.135 0.487 0.025 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.008 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 174.610 0.137 0.495 0.024 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 161.543 0.149 0.535 0.022 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.008 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 175.671 0.137 0.492 0.024 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (23 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.009 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 167.485 0.143 0.516 0.023 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.024 0.012 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 120.190 0.200 0.719 0.017 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (28 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 147.464 0.163 0.586 0.020 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 179.625 0.134 0.481 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (25 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There were 2 WARNINGs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 182.888 0.131 0.472 0.025 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 180.277 0.133 0.479 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.009 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 157.146 0.153 0.550 0.022 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.014 0.007 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 213.066 0.113 0.406 0.030 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: MTTK coupling is deprecated and will soon be removed 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.010 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 151.106 0.159 0.572 0.021 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.008 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 176.304 0.136 0.490 0.024 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (24 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 177.990 0.135 0.485 0.025 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 180.430 0.133 0.479 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 179.557 0.134 0.481 0.025 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.008 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 173.910 0.138 0.497 0.024 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 103: MTTK coupling is deprecated and will soon be removed 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 162.300 0.148 0.532 0.023 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.010 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 153.058 0.157 0.564 0.021 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (25 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 186.849 0.128 0.462 0.026 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 183.570 0.131 0.471 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 180.668 0.133 0.478 0.025 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 191.168 0.126 0.452 0.027 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 181.295 0.132 0.477 0.025 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 187.783 0.128 0.460 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: Center of mass removal not necessary for Andersen. All velocities of 103: coupled groups are rerandomized periodically, so flying ice cube errors 103: will not occur. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 194.298 0.124 0.445 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 165.670 0.145 0.522 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: Center of mass removal not necessary for Andersen. All velocities of 103: coupled groups are rerandomized periodically, so flying ice cube errors 103: will not occur. 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.009 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 170.451 0.141 0.507 0.024 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 179.929 0.133 0.480 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: Center of mass removal not necessary for Andersen. All velocities of 103: coupled groups are rerandomized periodically, so flying ice cube errors 103: will not occur. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 195.017 0.123 0.443 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 163.285 0.147 0.529 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 159.870 0.150 0.540 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 191.204 0.126 0.452 0.033 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (301 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 178.723 0.134 0.483 0.031 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.028 0.014 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 104.587 0.229 0.826 0.018 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (291 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.011 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 139.260 0.172 0.620 0.024 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 166.363 0.144 0.519 0.029 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (353 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 150.079 0.160 0.576 0.026 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.012 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 127.435 0.188 0.678 0.022 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (320 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.009 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 168.134 0.143 0.514 0.029 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 179.113 0.134 0.482 0.031 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (318 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 165.199 0.145 0.523 0.029 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.025 0.013 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 116.277 0.206 0.743 0.020 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (303 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There were 2 WARNINGs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.009 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 167.951 0.143 0.514 0.029 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 113.271 0.212 0.763 0.020 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (322 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 164.068 0.146 0.527 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 114.430 0.210 0.755 0.020 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (298 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 159.837 0.150 0.541 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.024 0.012 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 123.501 0.194 0.700 0.021 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (303 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 149.340 0.161 0.579 0.026 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 166.125 0.144 0.520 0.029 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (313 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.011 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 136.577 0.176 0.633 0.024 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.011 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 128.614 0.187 0.672 0.022 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (323 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 162.527 0.148 0.532 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 134.684 0.178 0.642 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (299 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.011 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 139.813 0.172 0.618 0.024 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 132.771 0.181 0.651 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (311 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 103: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (4484 ms total) 103: 103: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 194.071 0.124 0.445 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.014 0.007 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 204.644 0.117 0.422 0.028 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (20 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 188.692 0.127 0.458 0.026 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.007 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 200.566 0.120 0.431 0.028 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.014 0.007 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 208.579 0.115 0.414 0.029 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 189.178 0.127 0.457 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (20 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.014 0.007 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 216.101 0.111 0.400 0.030 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.010 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 152.524 0.157 0.566 0.021 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 159.320 0.151 0.542 0.022 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.007 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 198.473 0.121 0.435 0.028 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 191.168 0.126 0.452 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 182.536 0.131 0.473 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.009 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 170.177 0.141 0.508 0.024 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 189.708 0.127 0.455 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.007 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 199.766 0.120 0.433 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 194.666 0.123 0.444 0.027 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 195.234 0.123 0.443 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 189.440 0.127 0.456 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There were 2 WARNINGs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.013 0.007 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 220.517 0.109 0.392 0.031 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.008 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 175.062 0.137 0.494 0.024 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 166.584 0.144 0.519 0.023 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 193.377 0.124 0.447 0.027 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (22 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.007 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 196.416 0.122 0.440 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 194.968 0.123 0.443 0.027 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 189.306 0.127 0.456 0.026 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.010 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 153.562 0.156 0.563 0.021 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (23 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 133.908 0.179 0.645 0.019 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 189.056 0.127 0.457 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (25 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.007 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 201.038 0.119 0.430 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 184.173 0.130 0.469 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (21 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 189.452 0.127 0.456 0.033 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.011 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 138.238 0.174 0.625 0.024 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (336 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 185.248 0.130 0.466 0.032 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.012 199.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 125.744 0.191 0.687 0.022 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (290 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.009 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 168.267 0.143 0.513 0.029 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.011 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 130.110 0.184 0.664 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (295 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.008 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 175.191 0.137 0.493 0.030 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 148.720 0.161 0.581 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (309 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.009 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 155.245 0.155 0.557 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.012 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 125.647 0.191 0.688 0.022 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (304 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.008 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 175.495 0.137 0.492 0.030 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 134.291 0.179 0.643 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (321 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 134.678 0.178 0.642 0.023 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.010 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 142.864 0.168 0.605 0.025 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (301 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 163.628 0.147 0.528 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.011 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 128.573 0.187 0.672 0.022 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (295 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.010 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 150.313 0.160 0.575 0.026 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.012 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 126.200 0.190 0.685 0.022 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (300 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There were 2 WARNINGs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 163.990 0.146 0.527 0.028 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.015 0.008 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 190.289 0.126 0.454 0.033 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (293 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.009 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 157.010 0.153 0.550 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.011 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 129.669 0.185 0.666 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (304 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 177.575 0.135 0.487 0.031 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 131.578 0.182 0.657 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (294 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.010 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 141.152 0.170 0.612 0.025 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 147.361 0.163 0.586 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (299 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.024 0.012 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 122.873 0.195 0.703 0.021 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 132.483 0.181 0.652 0.023 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (293 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.009 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 155.198 0.155 0.557 0.027 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 148.448 0.162 0.582 0.026 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (293 ms) 103: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (4864 ms total) 103: 103: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Pull group 1 'FirstWaterMolecule' has 3 atoms 103: Pull group 2 'SecondWaterMolecule' has 3 atoms 103: Number of degrees of freedom in T-Coupling group System is 9.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: NVE simulation: will use the initial temperature of 2573.591 K for 103: determining the Verlet buffer size 103: 103: Pull group natoms pbc atom distance at start reference at t=0 103: 1 3 2 103: 2 3 5 1.112 nm 1.000 nm 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 3 of the 3 non-bonded parameter combinations 103: 103: Generated 3 of the 3 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.028 0.014 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 105.124 0.228 0.822 0.007 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.024 0.012 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 121.362 0.198 0.712 0.008 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (32 ms) 103: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (32 ms total) 103: 103: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Pull group 1 'FirstWaterMolecule' has 3 atoms 103: Pull group 2 'SecondWaterMolecule' has 3 atoms 103: Number of degrees of freedom in T-Coupling group System is 9.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: NVE simulation: will use the initial temperature of 2573.591 K for 103: determining the Verlet buffer size 103: 103: Pull group natoms pbc atom distance at start reference at t=0 103: 1 3 2 103: 2 3 5 1.112 nm 1.000 nm 103: 103: There were 2 NOTEs 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 3 of the 3 non-bonded parameter combinations 103: 103: Generated 3 of the 3 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/spc2.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.027 0.014 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 108.177 0.222 0.799 0.008 103: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 103: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 113.973 0.211 0.758 0.008 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (35 ms) 103: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (35 ms total) 103: 103: [----------] Global test environment tear-down 103: [==========] 94 tests from 4 test suites ran. (9471 ms total) 103: [ PASSED ] 94 tests. 103/104 Test #103: MdrunSimulatorComparison .................. Passed 9.49 sec test 104 Start 104: MdrunVirtualSiteTests 104: Test command: /build/reproducible-path/gromacs-2026.1/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.1/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 104: Working Directory: /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests 104: Test timeout computed to be: 600 104: [==========] Running 37 tests from 2 test suites. 104: [----------] Global test environment set-up. 104: [----------] 1 test from VirtualSiteVelocityTest 104: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 104: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 104: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 104: 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 3.0%. 104: The balanceable part of the MD step is 43%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 1.3%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.021 0.011 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 73.312 0.327 1.179 0.020 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: trr version: GMX_trn_file (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (19 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 1.4%. 104: The balanceable part of the MD step is 42%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.6%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.008 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 93.211 0.257 0.927 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (15 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 8.9%. 104: The balanceable part of the MD step is 36%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 3.2%. 104: 104: 104: NOTE: 46 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 96.189 0.250 0.898 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (14 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.018 0.009 198.6 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 85.500 0.281 1.011 0.024 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (24 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 46 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 198.6 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 89.656 0.268 0.964 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (24 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 90.480 0.265 0.955 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (21 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 199.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 88.523 0.271 0.976 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (18 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 46 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 98.643 0.243 0.876 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (18 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 46 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 198.3 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 91.069 0.264 0.949 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (23 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 0.8%. 104: The balanceable part of the MD step is 37%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.3%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 88.640 0.271 0.975 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (15 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 10.0%. 104: The balanceable part of the MD step is 48%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 4.8%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 95.530 0.251 0.904 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (12 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.015 0.008 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 101.701 0.236 0.850 0.028 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (18 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.018 0.009 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 87.805 0.273 0.984 0.024 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (19 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 90.976 0.264 0.950 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 98.953 0.243 0.873 0.027 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.017 0.009 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 89.935 0.267 0.961 0.025 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.014 0.007 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 113.209 0.212 0.763 0.031 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (16 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 94.924 0.253 0.910 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (17 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.018 0.009 199.3 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 85.135 0.282 1.015 0.024 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (23 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 95.296 0.252 0.907 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (21 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log). 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 94.339 0.254 0.916 0.026 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.1-Debian_2026.1_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (21 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (402 ms total) 104: 104: [----------] Global test environment tear-down 104: [==========] 37 tests from 2 test suites ran. (415 ms total) 104: [ PASSED ] 37 tests. 104/104 Test #104: MdrunVirtualSiteTests ..................... Passed 0.43 sec 100% tests passed, 0 tests failed out of 104 Label Time Summary: GTest = 180.00 sec*proc (97 tests) IntegrationTest = 83.42 sec*proc (30 tests) MpiTest = 103.44 sec*proc (24 tests) QuickGpuTest = 28.06 sec*proc (25 tests) SlowGpuTest = 135.01 sec*proc (15 tests) SlowTest = 83.74 sec*proc (14 tests) UnitTest = 12.84 sec*proc (53 tests) Total Test time (real) = 127.61 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.1/build/mpi/lib /usr/bin/make -j6 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2026.1/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.1 -B/build/reproducible-path/gromacs-2026.1/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.1/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2026.1/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.1/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.1-Debian_2026.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.1/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.1-1 -P /build/reproducible-path/gromacs-2026.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/lmfit/lmmin.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdmodule.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 2%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/binary_information.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/huffman.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 4%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdpoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmforceproviderbuilder.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 4%] Built target scanner cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 4%] Built target linearalgebra cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fmm/fmmforceprovider_stub.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 4%] Built target fmm /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_abf.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/fileio/h5md && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/fileio/h5md/h5md.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pull.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 4%] Built target h5md /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.1/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_alb.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 6%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/pullutil.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/programs /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_histogram.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 6%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/filenameoptionmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 8%] Built target pulling /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_opes.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 8%] Built target energyanalysis /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/options.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/taskassignment.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 8%] Built target options cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/constraintelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 8%] Built target taskassignment cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/nosehooverchains.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid_integrate.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvargrid_integrate.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/propagator.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/pullelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 12%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' [ 14%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.1/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.1 /build/reproducible-path/gromacs-2026.1/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.1/build/mpi' cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/veccompare.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/veccompare.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/utility/vecdump.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.1/src/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.1/src -I/build/reproducible-path/gromacs-2026.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.1/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.1/src/external -isystem /build/reproducible-path/gromacs-2026.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno TRUNCATED DUE TO SIZE LIMIT: 20971520 bytes